2BHE

HUMAN CYCLIN DEPENDENT PROTEIN KINASE 2 IN COMPLEX WITH THE INHIBITOR 5-BROMO-INDIRUBINE

PDB DOI: https://doi.org/10.2210/pdb2BHE/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2005-01-10 Released: 2005-03-09
Deposition Author(s): Schaefer, M., Jautelat, R., Brumby, T., Briem, H., Eisenbrand, G., Schwahn, S., Krueger, M., Luecking, U., Prien, O., Siemeister, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.322
R-Value Observed: 0.246

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

From the Insoluble Dye Indirubin Towards Highly Active, Soluble Cdk2-Inhibitors

Schaefer, M., Jautelat, R., Brumby, T., Briem, H., Eisenbrand, G., Schwahn, S., Krueger, M., Luecking, U., Prien, O., Siemeister, G.

(2005) Chembiochem 6: 531

PubMed: 15742375 Search on PubMed
DOI: https://doi.org/10.1002/cbic.200400108
Primary Citation of Related Structures:
2BHE, 2BHH

Organizational Affiliation

Medicinal Chemistry, Research Center Europe, Schering AG, 13342 Berlin, Germany. rolf.jautelat@schering.de

Macromolecule Content

Total Structure Weight: 34.32 kDa
Atom Count: 2,296
Modelled Residue Count: 274
Deposited Residue Count: 298
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELL DIVISION PROTEIN KINASE 2	A	298	Homo sapiens	Mutation(s): 0 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (UniProt)
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BRY Query on BRY 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]	(2Z)-5'-BROMO-2,3'-BIINDOLE-2',3(1H,1'H)-DIONE AMMONIATE C₁₆ H₉ Br N₂ O₂ IEQQJQHHJMQETK-YPKPFQOOSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
BRY	BindingDB: 2BHE	IC50: min: 80, max: 1000 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.322
R-Value Observed: 0.246
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.685	α = 90
b = 71.918	β = 90
c = 71.922	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-03-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-03-09
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-05-22
Changes: Data collection, Other, Refinement description
Version 1.4: 2019-07-24
Changes: Data collection
Version 1.5: 2024-05-08
Changes: Data collection, Database references, Other