Novobiocin

Summary

Novobiocin (CHEMBL36506) is an approved small-molecule antibacterial agent; indicated across 1 condition including osteomyelitis.

At a glance

• Status: Approved (max clinical phase 4)
• Modality: Small molecule
• Indications: 1 condition
• Clinical trials: 1
• Chemistry: 612.6 Da · C31H36N2O11

Identifiers

Drug identity and classification

Field	Value
ChEMBL ID	CHEMBL36506
Name	Novobiocin
Type	Small molecule
Max phase	4
FDA approved	no
PubChem CID	54675769
ChEBI	CHEBI:28368
Molecular formula	C31H36N2O11
Molecular weight	612.6
InChIKey	YJQPYGGHQPGBLI-KGSXXDOSSA-N

SMILES: CC1=C(C=CC2=C1OC(=O)C(=C2O)NC(=O)C3=CC(=C(C=C3)O)CC=C(C)C)O[C@H]4[C@@H]([C@@H]([C@H](C(O4)(C)C)OC)OC(=O)N)O

IUPAC name: [(3R,4S,5R,6R)-5-hydroxy-6-[4-hydroxy-3-[[4-hydroxy-3-(3-methylbut-2-enyl)benzoyl]amino]-8-methyl-2-oxochromen-7-yl]oxy-3-methoxy-2,2-dimethyloxan-4-yl] carbamate

ChEBI definition: A coumarin-derived antibiotic obtained from Streptomyces niveus.

Pharmacological roles (ChEBI): antibacterial agent, EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor, antimicrobial agent, hepatoprotective agent.

Other ChEBI roles (chemical / environmental): Escherichia coli metabolite.

Also known as: Albamycin t, Cathomycin, Novobiocin, Novobiocina, Novobiocine, novobiocin, SID26755282, NOVOBIOCINE, SID174006345, NOVOBIOCIN, Novobiocin; Albamycin, NOVOBIOCIN SODIUM

Parent form; salt/anhydrous children: CHEMBL3183453, CHEMBL3544972

Patent coverage: 3,610 distinct patent families (11,401 SureChEMBL compound mentions), from 2 matched compound structure(s). One matched structure accounts for 11,400 (100%) of the total. Mentions count patents naming the compound (not distinct inventions), so promiscuous / reference molecules inflate the mention figure — families are the dedup metric.

Targets

Targets

Primary targets (GtoPdb curated mechanism): the Cancer dependency column is the DepMap CRISPR fitness signal (% of screened cell lines dependent on the target).

Gene	Target	Action	pAffinity	Cancer dependency	UniProt
	DNA gyrase subunit B	Competitive	7.1

Broader ChEMBL bioactivity targets: 17 (assay-derived). Sample: DNA gyrase subunit B, DNA gyrase subunit B, DNA gyrase subunit B, DNA gyrase, Heat shock protein HSP90, DNA topoisomerase 4 subunit B, Vascular endothelial growth factor receptor 2, DNA gyrase, Topoisomerase IV, DNA gyrase subunit B, Albumin, DNA gyrase subunit A/DNA gyrase subunit B, Microtubule-associated protein 1 light chain 3 beta, Microtubule-associated protein 1 light chain 3 alpha, Broad substrate specificity ATP-binding cassette transporter ABCG2, DNA polymerase theta, DNA gyrase subunit B.

Bioactivity

ChEMBL activities: 60 potent at pChembl ≥ 5 of 82 total. Top 100 by potency (10 = 0.1 nM, 6 = 1 µM):

Target	pChembl	Type	Value	Unit	Activity ID
P0A0K8	9.19	IC50	0.65	nM	CHEMBL_ACT_25065658
P0AES4	8.35	IC50	4.52	nM	CHEMBL_ACT_25035771
P0AES6	8.15	Ki	7	nM	CHEMBL_ACT_16831571
P0AES6	8.15	Kd	7	nM	CHEMBL_ACT_16831572
P0A0K8	8	IC50	10	nM	CHEMBL_ACT_15642187
P0A0K8	8	IC50	10	nM	CHEMBL_ACT_16599335
P0A0K8	8	Ki	10	nM	CHEMBL_ACT_2236361
P9WG45	7.82	IC50	15	nM	CHEMBL_ACT_15105447
P9WG45	7.7	IC50	20	nM	CHEMBL_ACT_18679654
P0AES4	7.64	IC50	23	nM	CHEMBL_ACT_25072315
P0AES4	7.62	IC50	23.88	nM	CHEMBL_ACT_22767588
P0AES6	7.55	Kd	28	nM	CHEMBL_ACT_12149133
P0A0K8	7.52	IC50	30	nM	CHEMBL_ACT_15087667
P0A0K8	7.47	IC50	34	nM	CHEMBL_ACT_23174775
P0A4L9	7.43	IC50	37	nM	CHEMBL_ACT_3014616
P0A0K8	7.4	IC50	40	nM	CHEMBL_ACT_15640480
P0A0K8	7.4	IC50	40	nM	CHEMBL_ACT_16763408
P0A0K8	7.4	IC50	40	nM	CHEMBL_ACT_18903854
P0A0K8	7.39	IC50	41	nM	CHEMBL_ACT_16599233
P0A0K8	7.39	IC50	41	nM	CHEMBL_ACT_18066391
P0A0K8	7.39	IC50	41	nM	CHEMBL_ACT_18191762
P0A0K8	7.39	IC50	41	nM	CHEMBL_ACT_18427925
P0A0K8	7.39	IC50	41	nM	CHEMBL_ACT_19128582
P0A0K8	7.39	IC50	41	nM	CHEMBL_ACT_22387896
P0A0K8	7.39	IC50	41	nM	CHEMBL_ACT_22418917
P9WG45	7.34	IC50	46	nM	CHEMBL_ACT_14978302
P9WG45	7.34	IC50	46	nM	CHEMBL_ACT_15112917
P9WG45	7.34	IC50	46	nM	CHEMBL_ACT_15180679
P0C559	7.34	IC50	46	nM	CHEMBL_ACT_15183549
P9WG45	7.34	IC50	46	nM	CHEMBL_ACT_15753248
P9WG45	7.34	IC50	46	nM	CHEMBL_ACT_16447537
A0QNE0	7.34	IC50	46	nM	CHEMBL_ACT_16785245
P9WG45	7.34	IC50	46	nM	CHEMBL_ACT_16831359
P9WG45	7.3	IC50	50	nM	CHEMBL_ACT_13833936
P0AES4	7.1	IC50	80	nM	CHEMBL_ACT_15642186
P9WG45	7.07	IC50	85	nM	CHEMBL_ACT_18679657
P0AES4	7	IC50	100	nM	CHEMBL_ACT_3495059
P0A0K8	6.9	IC50	125	nM	CHEMBL_ACT_15087614
P0A0K8	6.9	IC50	125	nM	CHEMBL_ACT_18237893
P0AES4	6.84	IC50	144	nM	CHEMBL_ACT_18740465
P0AES6	6.81	IC50	154	nM	CHEMBL_ACT_3569055
P0AES4	6.78	IC50	168	nM	CHEMBL_ACT_22418900
P0AES4	6.77	IC50	170	nM	CHEMBL_ACT_15640440
P0AES6	6.77	IC50	170	nM	CHEMBL_ACT_16763430
P0AES6	6.77	IC50	170	nM	CHEMBL_ACT_18191758
P0AES6	6.77	IC50	170	nM	CHEMBL_ACT_18427859
P0AES4	6.77	IC50	170	nM	CHEMBL_ACT_19128590
P0AES4	6.77	IC50	170	nM	CHEMBL_ACT_22387925
P0AES4	6.77	IC50	170	nM	CHEMBL_ACT_23174740
P0C559	6.75	IC50	180	nM	CHEMBL_ACT_14978269
P0C559	6.75	IC50	180	nM	CHEMBL_ACT_15112949
P0C559	6.75	IC50	180	nM	CHEMBL_ACT_15180625
P0C559	6.75	IC50	180	nM	CHEMBL_ACT_15753728
P0C559	6.7	IC50	200	nM	CHEMBL_ACT_13834041
P0AES6	6.7	IC50	200	nM	CHEMBL_ACT_3569022
P0AES4	6.61	IC50	245	nM	CHEMBL_ACT_18740464
P0AES4	6.3	IC50	500	nM	CHEMBL_ACT_25072299
MAP1LC3A	5.12	Kd	7500	nM	CHEMBL_ACT_23271196
P0C1S7	5.1	IC50	7900	nM	CHEMBL_ACT_22462771
MAP1LC3A	5.06	Ki	8800	nM	CHEMBL_ACT_23271101

Target pathways

No target-pathway data for this drug (no mapped target genes).

Indications & clinical

Indications

Clinical trials

Total trials: 1.

Phase distribution

Phase	Trials
PHASE1	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT05687110	PHASE1	RECRUITING	Studying the Safety and Determining the Optimal Dose of Novobiocin in Patients With Tumors That Have Alterations in DNA Repair Genes

Clinical evidence (CIViC)

No CIViC predictive evidence (expected for non-precision-medicine drugs).

Pharmacology

Pharmacogenomics

No PharmGKB pharmacogenomic data curated for this drug.

Related molecules

Related molecules

No competitor molecules sharing a primary target (ChEMBL phase ≥2 or PubChem drug-class).