3R8M

CDK2 in complex with inhibitor L3-3

PDB DOI: https://doi.org/10.2210/pdb3R8M/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-03-24 Released: 2012-08-08
Deposition Author(s): Betzi, S., Alam, R., Han, H., Becker, A., Schonbrunn, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.239
R-Value Work: 0.204
R-Value Observed: 0.204

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure-guided optimization of novel CDK2 inhibitors discovered by high-throughput screening

Schonbrunn, E., Becker, A., Betzi, S., Alam, R., Han, H., Rawle, F., Katta, V., Jakkaraj, J., Chakrasali, R., Neelam, S., Hook, D., Tash, J., Georg, G.

To be published.

Macromolecule Content

Total Structure Weight: 35.03 kDa
Atom Count: 2,492
Modelled Residue Count: 286
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2	A	306	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24941
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Z19 Query on Z19 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1H-indazole-3-carbohydrazide C₈ H₈ N₄ O JOUPSJAGJHYWLM-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PO4 Query on PO4 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]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.239
R-Value Work: 0.204
R-Value Observed: 0.204
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.02	α = 90
b = 71.74	β = 90
c = 72.15	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
CNS	refinement
XDS	data reduction
XDS	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-08-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-08-08
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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Deposit Data

Help and Resources

3R8M

CDK2 in complex with inhibitor L3-3

Structure-guided optimization of novel CDK2 inhibitors discovered by high-throughput screening

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)