2VWW

ephB4 kinase domain inhibitor complex

PDB DOI: https://doi.org/10.2210/pdb2VWW/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2008-06-27 Released: 2008-07-08
Deposition Author(s): Read, J., Brassington, C.A., Green, I., McCall, E.J., Valentine, A.L., Barratt, D., Leach, A.G., Kettle, J.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.229
R-Value Work: 0.184
R-Value Observed: 0.186

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Inhibitors of the Tyrosine Kinase Ephb4. Part 1: Structure-Based Design and Optimization of a Series of 2,4-Bis-Anilinopyrimidines

Bardelle, C., Cross, D., Davenport, S., Kettle, J.G., Ko, E.J., Leach, A.G., Mortlock, A., Read, J., Roberts, N.J., Robins, P., Williams, E.J.

(2008) Bioorg Med Chem Lett 18: 2776

PubMed: 18434142 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2008.04.015
Primary Citation of Related Structures:
2VWU, 2VWV, 2VWW, 2VX0

PubMed Abstract:
A series of bis-anilinopyrimidines have been identified as potent inhibitors of the tyrosine kinase EphB4. Structural information from two alternative series identified from screening efforts was combined to identify the initial leads.

Organizational Affiliation

AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK.

Macromolecule Content

Total Structure Weight: 34.37 kDa
Atom Count: 2,126
Modelled Residue Count: 253
Deposited Residue Count: 302
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EPHRIN TYPE-B RECEPTOR 4	A	302	Homo sapiens	Mutation(s): 1 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P54760 (Homo sapiens) Explore P54760 Go to UniProtKB: P54760
PHAROS: P54760 GTEx: ENSG00000196411
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P54760
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7X2 Query on 7X2 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]	N'-(5-CHLORO-1,3-BENZODIOXOL-4-YL)-N-(3,4,5- TRIMETHOXYPHENYL)PYRIMIDINE-2,4-DIAMINE C₂₀ H₁₉ Cl N₄ O₅ HMKLUOPMOJOUDZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
7X2	BindingDB: 2VWW	IC50: 240 (nM) from 1 assay(s)
7X2	PDBBind: 2VWW	IC50: 240 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.229
R-Value Work: 0.184
R-Value Observed: 0.186
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.462	α = 90
b = 53.414	β = 111.38
c = 61.644	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-07-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-07-08
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: 2017-06-28
Changes: Data collection
Version 1.4: 2019-04-24
Changes: Data collection, Source and taxonomy
Version 1.5: 2019-05-08
Changes: Data collection, Experimental preparation
Version 1.6: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description