DNPH1

Summary

DNPH1 (2’-deoxynucleoside 5’-phosphate N-hydrolase 1, HGNC:21218) is a protein-coding gene on chromosome 6p21.1, encoding 5-hydroxymethyl-dUMP N-hydrolase (O43598). Part of a nucleotide salvage pathway that eliminates epigenetically modified 5-hydroxymethyl-dCMP (hmdCMP) in a two-step process entailing deamination to cytotoxic 5-hydroxymethyl-dUMP (hmdUMP), followed by its hydrolysis into 5-hydroxymethyluracil (hmU) and 2-deoxy-D-ribose 5-p….

This gene was identified on the basis of its stimulation by c-Myc protein. The latter is a transcription factor that participates in the regulation of cell proliferation, differentiation, and apoptosis. The exact function of this gene is not known but studies in rat suggest a role in cellular proliferation and c-Myc-mediated transformation. Two alternative transcripts encoding different proteins have been described.

Source: NCBI Gene 10591 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 37 total
• Druggable target: yes — 1 molecules with ChEMBL bioactivity
• MANE Select transcript: NM_006443

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21218
Approved symbol	DNPH1
Name	2’-deoxynucleoside 5’-phosphate N-hydrolase 1
Location	6p21.1
Locus type	gene with protein product
Status	Approved
Aliases	rcl, dJ330M21.3
Ensembl gene	ENSG00000112667
Ensembl biotype	protein_coding
OMIM	618762
Entrez	10591

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 10 protein_coding, 1 retained_intron

ENST00000230431, ENST00000393987, ENST00000505042, ENST00000509253, ENST00000878881, ENST00000912794, ENST00000912795, ENST00000912796, ENST00000912797, ENST00000912798, ENST00000945843

RefSeq mRNA: 2 — MANE Select: NM_006443 NM_006443, NM_199184

CCDS: CCDS43465, CCDS4891

Canonical transcript exons

ENST00000230431 — 4 exons

Exon	Start	End
ENSE00000751966	43226033	43226143
ENSE00000751969	43226327	43226395
ENSE00000850097	43225629	43225881
ENSE00002067621	43229261	43229481

Expression profiles

Bgee: expression breadth ubiquitous, 243 present calls, max score 97.43.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 27.2468 / max 182.9303, expressed in 1817 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
73674	26.6329	1816
73673	0.2702	95
73671	0.2108	88
73672	0.1328	49

Top tissues by expression

283 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	97.43	gold quality
mucosa of transverse colon	UBERON:0004991	97.00	gold quality
right adrenal gland cortex	UBERON:0035827	96.94	gold quality
right adrenal gland	UBERON:0001233	96.89	gold quality
left adrenal gland cortex	UBERON:0035825	96.82	gold quality
left adrenal gland	UBERON:0001234	96.80	gold quality
right lobe of liver	UBERON:0001114	96.30	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	96.23	gold quality
body of pancreas	UBERON:0001150	95.99	gold quality
small intestine Peyer’s patch	UBERON:0003454	95.36	gold quality
adrenal cortex	UBERON:0001235	95.28	gold quality
transverse colon	UBERON:0001157	95.02	gold quality
adult mammalian kidney	UBERON:0000082	94.97	gold quality
nucleus accumbens	UBERON:0001882	94.83	gold quality
nephron tubule	UBERON:0001231	94.38	gold quality
caudate nucleus	UBERON:0001873	94.38	gold quality
small intestine	UBERON:0002108	94.34	gold quality
metanephros cortex	UBERON:0010533	94.15	gold quality
adrenal gland	UBERON:0002369	94.02	gold quality
hindlimb stylopod muscle	UBERON:0004252	93.89	gold quality
body of stomach	UBERON:0001161	93.81	gold quality
apex of heart	UBERON:0002098	93.78	gold quality
muscle layer of sigmoid colon	UBERON:0035805	93.62	gold quality
right frontal lobe	UBERON:0002810	93.42	gold quality
lower esophagus mucosa	UBERON:0035834	93.42	gold quality
amygdala	UBERON:0001876	93.33	gold quality
duodenum	UBERON:0002114	93.11	gold quality
ileal mucosa	UBERON:0000331	93.09	gold quality
esophagus mucosa	UBERON:0002469	93.04	gold quality
left uterine tube	UBERON:0001303	93.00	gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-HCAD-6	yes	50.36
E-MTAB-6701	yes	46.26
E-HCAD-10	yes	33.13
E-CURD-112	yes	8.57
E-MTAB-10042	yes	5.50
E-GEOD-106540	no	105.95
E-CURD-120	no	31.08
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ETV1, MYC

miRNA regulators (miRDB)

14 targeting DNPH1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-6733-3P	99.54	67.80	1281
HSA-MIR-4489	99.50	65.56	785
HSA-MIR-4519	99.48	66.10	859
HSA-MIR-4251	99.40	69.19	3363
HSA-MIR-10522-5P	99.26	68.50	2087
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-6772-3P	97.04	65.89	784
HSA-MIR-664B-5P	96.74	67.50	509
HSA-MIR-5579-5P	96.32	68.54	730

Literature-anchored findings (GeneRIF, showing 4)

• characterization of the human Rcl gene, we cloned its promoter, Rcl is a bona fide target gene of ETV1. (PMID:18726892)
• analysis of human deoxynucleotide N-hydrolase Rcl and rat gene c6orf108 (PMID:20962348)
• Targeting the nucleotide salvage factor DNPH1 sensitizes BRCA-deficient cells to PARP inhibitors. (PMID:33833118)
• Human 2’-Deoxynucleoside 5’-Phosphate N-Hydrolase 1: The Catalytic Roles of Tyr24 and Asp80. (PMID:38350003)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	dnph1	ENSDARG00000075730
mus_musculus	Dnph1	ENSMUSG00000040658
rattus_norvegicus	Dnph1	ENSRNOG00000018397

Protein

Protein identifiers

5-hydroxymethyl-dUMP N-hydrolase — O43598 (reviewed: O43598)

Alternative names: 2’-deoxynucleoside 5’-phosphate N-hydrolase 1, c-Myc-responsive protein RCL

All UniProt accessions (2): O43598, H0Y8X4

UniProt curated annotations — full annotation on UniProt →

Function. Part of a nucleotide salvage pathway that eliminates epigenetically modified 5-hydroxymethyl-dCMP (hmdCMP) in a two-step process entailing deamination to cytotoxic 5-hydroxymethyl-dUMP (hmdUMP), followed by its hydrolysis into 5-hydroxymethyluracil (hmU) and 2-deoxy-D-ribose 5-phosphate (deoxyribosephosphate). Catalyzes the second step in that pathway, the hydrolysis of the N-glycosidic bond in hmdUMP, degrading this cytotoxic nucleotide to avoid its genomic integration.

Subunit / interactions. Monomer and homodimer.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Expressed at low levels in brain, colon, lung, peripheral blood leukocytes, placenta, small intestine, and thymus. Expressed at high levels in heart, kidney, liver, skeletal muscle and spleen. Overexpressed in a significant proportion of breast cancers.

Activity regulation. Inhibited by AMP and GMP.

Induction. Expression is induced by ETV1.

Similarity. Belongs to the 2’-deoxynucleoside 5’-phosphate N-hydrolase 1 family.

Isoforms (2)

UniProt ID	Names	Canonical?
O43598-1	1	yes
O43598-2	2

RefSeq proteins (2): NP_006434, NP_954653 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007710	Nucleoside_deoxyribTrfase	Family
IPR028607	DNPH1	Family
IPR051239	2’-dNMP_N-hydrolase	Family

Pfam: PF05014

Catalyzed reactions (Rhea), 1 shown:

• 5-hydroxymethyl-dUMP + H2O = 5-hydroxymethyluracil + 2-deoxy-D-ribose 5-phosphate (RHEA:77099)

UniProt features (36 total): helix 9, binding site 8, modified residue 7, strand 5, splice variant 2, turn 2, initiator methionine 1, chain 1, mutagenesis site 1

Structure

Experimental structures (PDB)

25 structures.

PDB	Method	Resolution (Å)
9DA2	X-RAY DIFFRACTION	1.13
9I58	X-RAY DIFFRACTION	1.21
9I57	X-RAY DIFFRACTION	1.22
4P5E	X-RAY DIFFRACTION	1.35
9DA6	X-RAY DIFFRACTION	1.35
8OSC	X-RAY DIFFRACTION	1.42
9DA1	X-RAY DIFFRACTION	1.47
9I6E	X-RAY DIFFRACTION	1.49
9S1N	X-RAY DIFFRACTION	1.5
9DA3	X-RAY DIFFRACTION	1.51
9S0O	X-RAY DIFFRACTION	1.51
9I3Q	X-RAY DIFFRACTION	1.6
8QHR	X-RAY DIFFRACTION	1.65
8OS9	X-RAY DIFFRACTION	1.7
9I9Q	X-RAY DIFFRACTION	1.72
9DA4	X-RAY DIFFRACTION	1.73
8RPS	X-RAY DIFFRACTION	1.75
9S1O	X-RAY DIFFRACTION	1.77
8QHQ	X-RAY DIFFRACTION	1.78
8RPT	X-RAY DIFFRACTION	1.95
9RPO	X-RAY DIFFRACTION	2.02
9RG8	X-RAY DIFFRACTION	2.07
8RQD	X-RAY DIFFRACTION	2.14
9IA6	X-RAY DIFFRACTION	2.21
9DA5	X-RAY DIFFRACTION	2.82

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O43598-F1	86.50	0.74

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (8): 27; 29; 30; 31; 98; 100; 104; 128 (in other chain)

Post-translational modifications (7): 2, 28, 98, 123, 128, 138, 169

Mutagenesis-validated functional residues (1):

Position	Phenotype
104	loss of deoxyribonucleoside 5’-monophosphate n-glycosidase activity.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-74259	Purine catabolism

MSigDB gene sets: 201 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, GOBP_EPITHELIUM_DEVELOPMENT, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_GROWTH, GOBP_CARBOHYDRATE_DERIVATIVE_CATABOLIC_PROCESS, CAIRO_PML_TARGETS_BOUND_BY_MYC_UP, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, GOBP_SMALL_MOLECULE_BIOSYNTHETIC_PROCESS, MARTINEZ_RB1_TARGETS_UP, RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP, GOBP_POSITIVE_REGULATION_OF_CELL_GROWTH, GOBP_AMIDE_METABOLIC_PROCESS

GO Biological Process (10): allantoin metabolic process (GO:0000255), purine nucleotide catabolic process (GO:0006195), deoxyribonucleoside monophosphate catabolic process (GO:0009159), positive regulation of cell growth (GO:0030307), epithelial cell differentiation (GO:0030855), nucleoside salvage (GO:0043174), dGMP catabolic process (GO:0046055), nucleoside metabolic process (GO:0009116), nucleotide metabolic process (GO:0009117), carbohydrate derivative metabolic process (GO:1901135)

GO Molecular Function (7): identical protein binding (GO:0042802), protein homodimerization activity (GO:0042803), 5-hydroxymethyl-dUMP N-hydrolase activity (GO:0070694), protein binding (GO:0005515), hydrolase activity (GO:0016787), hydrolase activity, acting on glycosyl bonds (GO:0016798), hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)

GO Cellular Component (4): nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829), extracellular exosome (GO:0070062)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Nucleotide catabolism	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
metabolic process	2
cellular anatomical structure	2
purine nucleotide metabolic process	1
nucleotide catabolic process	1
purine-containing compound catabolic process	1
nucleoside monophosphate catabolic process	1
regulation of cell growth	1
cell growth	1
positive regulation of growth	1
positive regulation of cellular process	1
cell differentiation	1
epithelium development	1
nucleoside biosynthetic process	1
metabolic compound salvage	1
purine deoxyribonucleotide catabolic process	1
purine deoxyribonucleoside monophosphate catabolic process	1
dGMP metabolic process	1
nucleobase-containing small molecule metabolic process	1
carbohydrate derivative metabolic process	1
nucleoside phosphate metabolic process	1
protein binding	1
identical protein binding	1
protein dimerization activity	1
hydrolase activity, hydrolyzing N-glycosyl compounds	1
binding	1
catalytic activity	1
hydrolase activity	1
hydrolase activity, acting on glycosyl bonds	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cytoplasm	1
extracellular vesicle	1

Protein interactions and networks

STRING

504 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DNPH1	RWDD1	Q9H446	497
DNPH1	PCNP	Q8WW12	487
DNPH1	RABGGTB	P53611	458
DNPH1	DCLK3	Q9C098	453
DNPH1	RAD51AP2	Q09MP3	452
DNPH1	KCNK2	O95069	439
DNPH1	SRPRA	P08240	411
DNPH1	CFP	P27918	410
DNPH1	B4GALT2	O60909	407
DNPH1	B4GALT3	O60512	374
DNPH1	PEX39	Q5I0X4	373
DNPH1	ZBED8L	Q8TCP9	371
DNPH1	PRAP1	Q96NZ9	369
DNPH1	NANS	Q9NR45	365
DNPH1	RCL1	Q9Y2P8	358

IntAct

37 interactions, top by confidence:

A	B	Type	Score
DNPH1	DNPH1	psi-mi:“MI:0915”(physical association)	0.740
DNPH1	DDIT4L	psi-mi:“MI:0915”(physical association)	0.560
PRKCA	DNPH1	psi-mi:“MI:0915”(physical association)	0.560
DNPH1	YWHAG	psi-mi:“MI:0915”(physical association)	0.560
DNPH1	SETDB1	psi-mi:“MI:0915”(physical association)	0.560
KAT5	DNPH1	psi-mi:“MI:0915”(physical association)	0.560
LMO3	DNPH1	psi-mi:“MI:0915”(physical association)	0.560
TERF1	DNPH1	psi-mi:“MI:0915”(physical association)	0.510
DNPH1	POT1	psi-mi:“MI:0915”(physical association)	0.370
PILRA	DNPH1	psi-mi:“MI:0915”(physical association)	0.370
Brca1	SMCHD1	psi-mi:“MI:0914”(association)	0.350
PRNP	CARNS1	psi-mi:“MI:0914”(association)	0.350
PRNP	WDR91	psi-mi:“MI:0914”(association)	0.350
SMPD2	A2ML1	psi-mi:“MI:0914”(association)	0.350
LARP7	SBNO1	psi-mi:“MI:2364”(proximity)	0.270
XRCC6	PSMD11	psi-mi:“MI:2364”(proximity)	0.270
FTSJ1	DNPH1	psi-mi:“MI:0915”(physical association)	0.000
DNPH1	TERF1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (20): DNPH1 (Two-hybrid), DNPH1 (Two-hybrid), DNPH1 (Affinity Capture-MS), DNPH1 (Two-hybrid), DDIT4L (Two-hybrid), DNPH1 (Affinity Capture-MS), DNPH1 (Proximity Label-MS), DNPH1 (Affinity Capture-MS), DNPH1 (Affinity Capture-MS), DNPH1 (Affinity Capture-MS), DNPH1 (Proximity Label-MS), DNPH1 (Two-hybrid), DNPH1 (Two-hybrid), DNPH1 (Co-fractionation), DNPH1 (Co-fractionation)

ESM2 similar proteins: A0LD71, A1A8Z3, A6U6V4, A6V9L0, A7RLE5, B2VBT3, B3SAE4, B4RPZ2, B4SZF9, B4TC11, B5BC59, B5F034, B5QX27, B5R6A2, B6PLN3, B7MGK7, B7MPN4, B7N9Z2, B7ULM3, B8A556, C1BW56, C6DCF2, O35820, O43598, O88618, O95954, P0AFA5, P0AFA6, P21865, P24519, P38035, P53603, Q0TJV1, Q1REI1, Q20Z33, Q2NUL1, Q32IH8, Q3MBV3, Q4S2L4, Q57RK0

Diamond homologs: A1RW47, A7RLE5, B3SAE4, B6PLN3, B8A556, C1BW56, O35820, O43598, Q12UY1, Q24FH8, Q3A6G9, Q46CC9, Q4S2L4, Q80VJ3, Q8PW97, Q8TTA0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

37 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	28
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

584 predictions. Top by Δscore:

Variant	Effect	Δscore
6:43226141:CCA:C	acceptor_gain	1.0000
6:43226142:CA:C	acceptor_gain	1.0000
6:43226142:CAC:C	acceptor_gain	1.0000
6:43226144:C:CC	acceptor_gain	1.0000
6:43226393:CCC:C	acceptor_gain	1.0000
6:43226394:CCC:C	acceptor_gain	1.0000
6:43226395:CCTGT:C	acceptor_loss	1.0000
6:43226396:C:CA	acceptor_loss	1.0000
6:43226396:C:CC	acceptor_gain	1.0000
6:43229260:CCG:C	donor_gain	1.0000
6:43226032:CCG:C	donor_gain	0.9900
6:43226140:ACCA:A	acceptor_gain	0.9900
6:43226141:CCAC:C	acceptor_gain	0.9900
6:43226143:ACTG:A	acceptor_loss	0.9900
6:43226319:CCACT:C	donor_loss	0.9900
6:43226320:CACTC:C	donor_loss	0.9900
6:43226321:ACTCA:A	donor_loss	0.9900
6:43226322:CT:C	donor_loss	0.9900
6:43226323:T:TC	donor_loss	0.9900
6:43226324:CA:C	donor_loss	0.9900
6:43226325:A:AC	donor_gain	0.9900
6:43226326:C:CC	donor_gain	0.9900
6:43226326:C:G	donor_loss	0.9900
6:43226394:CC:C	acceptor_gain	0.9900
6:43226395:CCTG:C	acceptor_gain	0.9900
6:43226398:G:GC	acceptor_gain	0.9900
6:43229255:CCTCA:C	donor_loss	0.9900
6:43229256:CTCA:C	donor_loss	0.9900
6:43229257:TCACC:T	donor_loss	0.9900
6:43229258:CACCG:C	donor_loss	0.9900

AlphaMissense

1098 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:43226052:G:C	F119L	0.986
6:43226052:G:T	F119L	0.986
6:43226054:A:G	F119L	0.986
6:43226058:G:C	C117W	0.972
6:43226097:C:A	E104D	0.972
6:43226097:C:G	E104D	0.972
6:43226060:A:G	C117R	0.971
6:43226125:G:A	T95I	0.970
6:43229296:G:A	T54I	0.969
6:43226125:G:T	T95K	0.966
6:43226140:A:T	V90D	0.963
6:43229377:C:T	G27E	0.960
6:43229382:G:C	F25L	0.959
6:43229382:G:T	F25L	0.959
6:43229384:A:G	F25L	0.959
6:43226134:G:T	A92E	0.957
6:43229373:G:C	S28R	0.956
6:43229373:G:T	S28R	0.956
6:43229375:T:G	S28R	0.956
6:43226059:C:T	C117Y	0.951
6:43226135:C:G	A92P	0.950
6:43229374:C:A	S28I	0.950
6:43226111:C:G	G100R	0.946
6:43226333:C:G	A87P	0.946
6:43226131:T:A	E93V	0.945
6:43225866:A:G	I131T	0.941
6:43229383:A:G	F25S	0.941
6:43226110:C:T	G100D	0.938
6:43229378:C:A	G27W	0.938
6:43226086:G:T	A108D	0.937

dbSNP variants (sampled 300 via entrez): RS1000202039 (6:43231028 A>G), RS1000658896 (6:43230743 C>A,T), RS1000816985 (6:43226474 C>A,G,T), RS1000857876 (6:43226776 C>T), RS1002404595 (6:43227287 C>T), RS1002781280 (6:43227133 C>T), RS1003372941 (6:43228488 C>A,G), RS1003437420 (6:43229807 G>C,T), RS1003506390 (6:43228684 G>C), RS1003814700 (6:43228873 G>A), RS1004509456 (6:43231102 G>A,C), RS1004515413 (6:43227450 TCC>T), RS1004853954 (6:43229187 G>A,C,T), RS1004930254 (6:43229432 G>A,C), RS1005383594 (6:43225817 C>G,T)

Disease associations

OMIM: gene MIM:618762 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST008899_1	Adult hearing difficulty	6.000000e-21

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3351218 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 165,316 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

Molecule	Name	Phase	Patents
CHEMBL752	ADENOSINE PHOSPHATE	4	165,316

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

37 potent at pChembl≥5 of 47 total, top 37 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
6.37	Kd	430	nM	CHEMBL6176298
6.30	Ki	500	nM	CHEMBL3331365
6.30	Ki	500	nM	CHEMBL3331381
6.24	Kd	570	nM	CHEMBL6176298
6.22	Kd	600	nM	CHEMBL3274191
6.21	Ki	610	nM	CHEMBL6177387
5.96	Ki	1100	nM	CHEMBL3331379
5.89	Ki	1300	nM	CHEMBL3331375
5.89	IC50	1300	nM	CHEMBL3274191
5.89	Kd	1300	nM	CHEMBL6176738
5.86	Kd	1375	nM	CHEMBL5653589
5.85	Ki	1400	nM	CHEMBL3356090
5.82	Ki	1500	nM	CHEMBL3331366
5.82	Ki	1500	nM	CHEMBL3331371
5.82	Ki	1500	nM	CHEMBL3331380
5.82	IC50	1500	nM	CHEMBL6176298
5.80	Ki	1600	nM	CHEMBL3331378
5.77	Ki	1700	nM	CHEMBL3331373
5.72	Ki	1900	nM	CHEMBL519155
5.71	ED50	1937	nM	CHEMBL5653589
5.68	Ki	2100	nM	CHEMBL3331368
5.62	Ki	2400	nM	CHEMBL3331367
5.60	Ki	2500	nM	CHEMBL3331377
5.57	Ki	2700	nM	CHEMBL3331370
5.55	Ki	2800	nM	CHEMBL3331362
5.54	Ki	2900	nM	CHEMBL3329986
5.54	Ki	2850	nM	CHEMBL6175626
5.48	Ki	3300	nM	CHEMBL6176738
5.43	Ki	3700	nM	CHEMBL3331372
5.43	Ki	3670	nM	CHEMBL6172195
5.42	Ki	3800	nM	CHEMBL3331374
5.38	Ki	4200	nM	CHEMBL3331363
5.29	Ki	5170	nM	CHEMBL6168678
5.29	Ki	5140	nM	CHEMBL6162899
5.28	Ki	5300	nM	CHEMBL3331369
5.20	Kd	6300	nM	CHEMBL6176336
5.19	Ki	6500	nM	CHEMBL6176941

PubChem BioAssay actives

22 with measured affinity, of 27 total; 22 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
[(2R,3S,4R,5R)-3,4-dihydroxy-5-[6-(3-phenylphenyl)purin-9-yl]oxolan-2-yl]methyl dihydrogen phosphate	1187163: Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	ki	0.5000	uM
[(2R,3S,4R,5R)-3,4-dihydroxy-5-[6-[3-(6-methoxynaphthalen-2-yl)phenyl]purin-9-yl]oxolan-2-yl]methyl dihydrogen phosphate	1187163: Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	ki	0.5000	uM
[(2R,3S,4R,5R)-5-[6-(3-bromophenyl)purin-9-yl]-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen phosphate	1187163: Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	ki	1.1000	uM
[(2R,3S,4R,5R)-5-[6-(5-chlorothiophen-2-yl)purin-9-yl]-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen phosphate	1187163: Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	ki	1.3000	uM
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2148257: Binding affinity to human DNPH1 incubated for 45 mins by Kinobead based pull down assay	kd	1.3750	uM
[(2R,3S,4R,5R)-5-[6-(3-dibenzothiophen-4-ylphenyl)purin-9-yl]-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen phosphate	1187163: Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	ki	1.4000	uM
[(2R,3S,4R,5R)-3,4-dihydroxy-5-(6-phenylpurin-9-yl)oxolan-2-yl]methyl dihydrogen phosphate	1187163: Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	ki	1.5000	uM
4-[3-[9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]purin-6-yl]phenyl]benzoic acid	1187163: Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	ki	1.5000	uM
[(2R,3S,4R,5R)-3,4-dihydroxy-5-[6-(4-hydroxyphenyl)purin-9-yl]oxolan-2-yl]methyl dihydrogen phosphate	1187163: Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	ki	1.5000	uM
[(2R,3S,4R,5R)-5-[6-(5-bromo-3-pyridinyl)purin-9-yl]-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen phosphate	1187163: Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	ki	1.6000	uM
[(2R,3S,4R,5R)-5-[6-(furan-3-yl)purin-9-yl]-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen phosphate	1187163: Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	ki	1.7000	uM
[(2R,3S,4R,5R)-5-[6-(benzylamino)purin-9-yl]-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen phosphate	1187163: Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	ki	1.9000	uM
[(2R,3S,4R,5R)-5-[6-(4-cyanophenyl)purin-9-yl]-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen phosphate	1187163: Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	ki	2.1000	uM
methyl 3-[9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]purin-6-yl]benzoate	1187163: Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	ki	2.4000	uM
[(2R,3S,4R,5R)-3,4-dihydroxy-5-[6-(1H-indol-6-yl)purin-9-yl]oxolan-2-yl]methyl dihydrogen phosphate	1187163: Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	ki	2.5000	uM
4-[9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]purin-6-yl]benzoic acid	1187163: Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	ki	2.7000	uM
[(2R,3S,4R,5R)-3,4-dihydroxy-5-(6-naphthalen-2-ylpurin-9-yl)oxolan-2-yl]methyl dihydrogen phosphate	1187163: Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	ki	2.8000	uM
3-[9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]purin-6-yl]benzoic acid	1187163: Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	ki	2.9000	uM
4-[4-[9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]purin-6-yl]anilino]-4-oxobutanoic acid	1187163: Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	ki	3.7000	uM
[(2R,3S,4R,5R)-5-[6-(5-formylfuran-2-yl)purin-9-yl]-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen phosphate	1187163: Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	ki	3.8000	uM
[(2R,3S,4R,5R)-5-[6-(3-cyanophenyl)purin-9-yl]-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen phosphate	1187163: Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	ki	4.2000	uM
[(2R,3S,4R,5R)-3,4-dihydroxy-5-[6-(3-nitrophenyl)purin-9-yl]oxolan-2-yl]methyl dihydrogen phosphate	1187163: Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	ki	5.3000	uM

CTD chemical–gene interactions

62 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, decreases expression, increases expression	4
Valproic Acid	decreases expression, affects expression	4
sodium arsenite	affects cotreatment, decreases expression	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression, decreases expression	2
Benzo(a)pyrene	decreases expression, increases methylation	2
Cocaine	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tobacco Smoke Pollution	decreases expression	2
aristolochic acid I	decreases expression	1
GSK-J4	decreases expression	1
FR900359	increases phosphorylation	1
testosterone enanthate	affects expression	1
triphenyl phosphate	increases expression	1
methylselenic acid	decreases expression	1
sodium arsenate	decreases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
cobaltous chloride	decreases expression	1
zinc chromate	decreases expression, increases abundance	1
manganese chloride	decreases expression	1
4-hydroxy-2-nonenal	decreases expression	1
periodate-oxidized adenosine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
chromium hexavalent ion	decreases expression, increases abundance	1
K 7174	decreases expression	1
bisphenol B	increases expression	1
dorsomorphin	decreases expression, affects cotreatment	1
jinfukang	affects cotreatment, increases expression	1
LDN 193189	affects cotreatment, increases expression	1
NSC 689534	affects binding, decreases expression	1
MT19c compound	decreases expression	1

ChEMBL screening assays

13 unique, capped per target: 13 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL3362303	Binding	Inhibition of human DNPH1 assessed as 2-deoxyribose 5-phosphate production by spectrophotometrically	6-(Hetero)Arylpurine nucleotides as inhibitors of the oncogenic target DNPH1: synthesis, structural studies and cytotoxic activities. — Eur J Med Chem

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.