6JGM | pdb_00006jgm

Crystal structure of CDK2 IN complex with Inhibitor NU-6140

PDB DOI: https://doi.org/10.2210/pdb6JGM/pdb

Classification: CELL CYCLE/INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2019-02-14 Released: 2020-02-26
Deposition Author(s): SumalathaRani, T., Narasimharao, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.290 (Depositor), 0.288 (DCC)
R-Value Work:
0.214 (Depositor), 0.223 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of CDK2 IN complex with Inhibitor NU-6140

SumalathaRani, T., Narasimharao, K.

To be published.

Macromolecule Content

Total Structure Weight: 34.49 kDa
Atom Count: 2,324
Modeled Residue Count: 279
Deposited Residue Count: 299
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2	A	299	Homo sapiens	Mutation(s): 0 Gene Names: CDK2 EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens) Explore P24941 Go to UniProtKB: P24941
PHAROS: P24941 GTEx: ENSG00000123374
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24941
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AQG Query on AQG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-{[6-(cyclohexylmethoxy)-7H-purin-2-yl]amino}-N,N-diethylbenzamide C₂₃ H₃₀ N₆ O₂ XHEQSRJCJTWWAH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
AQG	BindingDB: 6JGM	IC50: min: 400, max: 4.07e+5 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.290 (Depositor), 0.288 (DCC)
R-Value Work: 0.214 (Depositor), 0.223 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.491	α = 90
b = 72.01	β = 90
c = 72.33	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-02-26

Deposition Author(s):

SumalathaRani, T.

Narasimharao, K.

Revision History (Full details and data files)

Version 1.0: 2020-02-26
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.