CDK9

Cyclin-dependent kinase 9

237,899 patent compounds predicted against CDK9, 135,371 high-confidence (nearest known ligand ≥ 0.5)

Top predicted compounds (top 20 by supporting neighbours, then confidence)

Compound	Confidence	Supporting neighbours
SCHEMBL268925	0.50	17/20
SCHEMBL269583	0.50	17/20
SCHEMBL102235	1.00	13/20
SCHEMBL102955	1.00	13/20
Bms-387032 (SCHEMBL187401)	1.00	13/20
SCHEMBL102656	0.79	13/20
SCHEMBL102951	0.76	13/20
SCHEMBL102660	0.75	13/20
SCHEMBL102233	1.00	12/20
SCHEMBL103266	0.79	12/20
SCHEMBL102507	0.78	12/20
SCHEMBL102650	0.76	12/20
SCHEMBL21498	0.35	12/20
SCHEMBL103265	1.00	11/20
SCHEMBL102984	0.77	11/20
SCHEMBL102952	0.76	11/20
Alvocidib (SCHEMBL3651)	1.00	10/20
Alvocidib (SCHEMBL3652)	1.00	10/20
SCHEMBL102236	0.75	10/20
SCHEMBL102764	0.75	10/20

Germline variants in CDK9 on Sugi Variant → ClinVar classifications, population frequency, and predictor agreement (AlphaMissense, SaProt, REVEL) Full CDK9 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

Clinical trials — most relevant to CDK9 by text similarity (a relevance ranking, not an exhaustive list)

Trial	Phase	Status
Clinical and Pharmacoeconomic Assessment of CDK4/6 Inhibitors for Treatment of Breast Cancer in Egypt	PHASE4	COMPLETED
A Phase 3 Study Comparing Dinaciclib Versus Ofatumumab in Patients With Refractory Chronic Lymphocytic Leukemia (P07714)	PHASE3	COMPLETED
A Study of Palbociclib (PD-0332991) + Letrozole vs. Letrozole For 1st Line Treatment Of Postmenopausal Women With ER+/HER2- Advanced Breast Cancer (PALOMA-2)	PHASE3	COMPLETED
Implementing Geriatric Assessment for Dose Optimization of Cyclin-dependent Kinase (CDK) 4/6-inhibitors in Older Breast Cancer Patients	PHASE3	RECRUITING
A Study of Tersolisib (LY4064809/STX-478) With Other Anti-Cancer Treatments in Participants With Advanced Breast Cancer With a Genetic Change (PIK3CA)	PHASE3	RECRUITING
Efficacy Study Of P276-00 In Subjects Of Malignant Melanoma Positive For Cyclin D1 Expression	PHASE2	COMPLETED
CDK 4/6 Inhibitor, Ribociclib, With Adjuvant Endocrine Therapy for ER-positive Breast Cancer	PHASE2	ACTIVE_NOT_RECRUITING
To Reverse ENDocrine Resistance Trial - PD 0332991 Monotherapy vs PD 0332991 in Combination With the Endocrine Therapy	PHASE2	COMPLETED
A Phase II Study of AT7519M, a CDK Inhibitor, in Patients With Relapsed and/or Refractory Chronic Lymphocytic Leukemia	PHASE2	COMPLETED
Palbociclib and Sasanlimab for the Treatment of Advanced Clear Cell Renal Cell Carcinoma (ccRCC) or Papillary Renal Cell Carcinoma (pRCC)	PHASE1/PHASE2	RECRUITING
Palbociclib With Everolimus + Exemestane In BC	PHASE1/PHASE2	COMPLETED
Study of SLS009 (Formerly GFH009) a Potent Highly Selective CDK9 Inhibitor in Patients With Hematologic Malignancies and High-Risk Newly Diagnosed AML	PHASE1/PHASE2	RECRUITING
Study of the CDK4/6 Inhibitor Abemaciclib in Solid Tumors Harboring Genetic Alterations in Genes Encoding D-Type Cyclins or Amplification of CDK4 or CDK6	PHASE2	RECRUITING
Determinants of Resistance to Endocrine Therapy and a Cyclin-dependent Kinases 4 and 6 (CDK4/6) Inhibitor for HR+ MBC	PHASE2	ACTIVE_NOT_RECRUITING
A First-in-Human Study of CDK-002 (exoSTING) in Subjects With Advanced/Metastatic, Recurrent, Injectable Solid Tumors	PHASE1/PHASE2	COMPLETED
Evexomostat Plus PI3K or AKT Inhibitor and Fulvestrant in Patients With a PI3K Alteration and HR+/Her2- Breast Cancer	PHASE1/PHASE2	RECRUITING
A Study of Palbociclib in Combination With Bazedoxifene in Hormone Receptor Positive Breast Cancer	PHASE1/PHASE2	COMPLETED
BAY 1000394 for MCL-1-, MYC-, and CCNE1-Amplified Tumors	PHASE2	WITHDRAWN
TQB3616 Capsules Combined With Abiraterone Acetate Plus Prednisone in Metastatic Castration-Resistant Prostate Cancer	PHASE2	UNKNOWN
Cyclin Dependent Kinase (CDK)4/6 Inhibitor, PD0332991 in Advanced Non-small Cell Lung Cancer NSCLC.	PHASE2	COMPLETED
A Clinical Trial of TQB3909 Tablets in Patients With Breast Cancer	PHASE1/PHASE2	UNKNOWN
Dinaciclib, Bortezomib, and Dexamethasone in Treating Patients With Relapsed Multiple Myeloma	PHASE1	COMPLETED
A Study of PRT2527 in Participants With Advanced Solid Tumors	PHASE1	COMPLETED
TSL2109 Capsules in Advanced Solid Tumor Patients: Safety, Tolerability, PK and Preliminary Efficacy	PHASE1	RECRUITING
Study of AC699 in Patients With Estrogen Receptor Positive/Human Epidermal Growth Factor Receptor 2 Negative (ER+/HER2-) Locally Advanced or Metastatic Breast Cancer	PHASE1	ACTIVE_NOT_RECRUITING
Real-World Clinical Outcomes and Toxicity in Metastatic Breast Cancer Patients Treated With First or Second Line CDK 4/6 Inhibitors and Endocrine Therapy	nan	COMPLETED
Study Of Real-World Evidence In Patients Treated With Palbociclib During a 2.5 Years Follow-Up Period	nan	UNKNOWN
The SONImage Study	nan	ACTIVE_NOT_RECRUITING
EVERST- Everolimus After Alpelisib in Women With Hormone Receptor-positive (HR+) Metastatic Breast Cancer (MBC)	nan	RECRUITING
Advanced Breast Cancer Study of CDK4/6 Inhibitor Combined With Endocrine Therapy Endocrine Therapy in HR+/HER2- Advanced Breast Cancer	nan	UNKNOWN

Related proteins — ESM-2 sequence neighbours (a CDK9 binder may also engage these)

Protein	Name	Similarity
Q99J95	—	1.000	Q99J95 →
Q5EAB2	—	1.000	Q5EAB2 →
Q641Z4	—	0.999	Q641Z4 →
Q7ZX42	—	0.999	Q7ZX42 →
Q7SXE8	—	0.998	Q7SXE8 →
Q6GLD8	—	0.997	Q6GLD8 →
Q4V862	—	0.996	Q4V862 →
Q12126	—	0.993	Q12126 →
G5EFV5	—	0.993	G5EFV5 →
Q5ZKN1	—	0.992	Q5ZKN1 →
A8WIP6	—	0.992	A8WIP6 →
O13958	—	0.990	O13958 →
Q6CCB0	—	0.990	Q6CCB0 →
O44408	—	0.989	O44408 →
Q8SW92	—	0.989	Q8SW92 →
Q9C9U2	—	0.989	Q9C9U2 →
Q4WQR3	—	0.988	Q4WQR3 →
Q3TZA2	—	0.988	Q3TZA2 →
MAPK13	Mitogen-activated protein kinase 13	0.988	landscape →
Q03147	—	0.988	Q03147 →
O60145	—	0.987	O60145 →
G4N374	—	0.987	G4N374 →
Q8CEQ0	—	0.987	Q8CEQ0 →
B0Y4X4	—	0.987	B0Y4X4 →
A8XA58	—	0.987	A8XA58 →
Q9Z1B7	—	0.987	Q9Z1B7 →
A0A194WDG1	—	0.987	A0A194WDG1 →
P20911	—	0.987	P20911 →
Q9LMT0	—	0.986	Q9LMT0 →
P51952	—	0.986	P51952 →