6W9E

Crystal Structure of Human CDK9/cyclinT1 in complex with MC180295

• PDB DOI: https://doi.org/10.2210/pdb6W9E/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2020-03-22 Released: 2021-09-01 
• Deposition Author(s): Zhang, P., Wu, J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), American Cancer Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.221 
• R-Value Work: 0.172 
• R-Value Observed: 0.175 

Starting Model: experimental

Literature

Comparative Modeling of CDK9 Inhibitors to Explore Selectivity and Structure-Activity Relationships

Kirubakaran, P., Morton, G., Zhang, P., Zhang, H., Abou-Gharbia, M., Issa, J., Wu, J., Childers, W., Karanicolas, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 69.74 kDa 
• Atom Count: 4,688 
• Modelled Residue Count: 563 
• Deposited Residue Count: 589 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 9	A	330	Homo sapiens	Mutation(s): 0  Gene Names: CDK9, CDC2L4, TAK EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P50750 (Homo sapiens) Explore P50750  Go to UniProtKB:  P50750
PHAROS:  P50750 GTEx:  ENSG00000136807

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-T1	B	259	Homo sapiens	Mutation(s): 3  Gene Names: CCNT1
UniProt & NIH Common Fund Data Resources
Find proteins for O60563 (Homo sapiens) Explore O60563  Go to UniProtKB:  O60563
PHAROS:  O60563 GTEx:  ENSG00000129315

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TOJ	E [auth A], F [auth A]	(4-amino-2-{[(1R,2R,4S)-bicyclo[2.2.1]heptan-2-yl]amino}-1,3-thiazol-5-yl)(2-nitrophenyl)methanone C17 H18 N4 O3 S JRNXAQINDCOHGS-HOSYDEDBSA-N
TO7	C [auth A], D [auth A]	(4-amino-2-{[(1S,2S,4R)-bicyclo[2.2.1]heptan-2-yl]amino}-1,3-thiazol-5-yl)(2-nitrophenyl)methanone C17 H18 N4 O3 S JRNXAQINDCOHGS-SCVCMEIPSA-N
PO4	G [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Binding Affinity Annotations
ID	Source	Binding Affinity
TO7	BindingDB:  6W9E	IC50: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.221 
• R-Value Work: 0.172 
• R-Value Observed: 0.175 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.34	α = 90
b = 173.34	β = 90
c = 97.368	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-09-01 
Deposition Author(s): Zhang, P., Wu, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM119560
American Cancer Society	United States	RSG-15-167-01-DMC

Revision History  

• Version 1.0: 2021-09-01
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary