Macromolecule Content

Total Structure Weight: 66.34 kDa
Atom Count: 4,329
Modelled Residue Count: 527
Deposited Residue Count: 572
Unique protein chains: 1

5T0P

c-Src kinase domain in complex with Rao-IV-151

PDB DOI: 10.2210/pdb5T0P/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Gallus gallus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-08-16 Released: 2017-08-23
Deposition Author(s): Dieter, E.M., Merritt, E.A., Maly, D.J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.323
R-Value Work: 0.264
R-Value Observed: 0.267

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

A chemical genetic method for conformation-selective kinase inhibition

Register, A.C., Maly, D.J.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A, B	286	Gallus gallus	Mutation(s): 1 Gene Names: SRC EC: 2.7.10.2
UniProt
Find proteins for P00523 (Gallus gallus) Explore P00523 Go to UniProtKB: P00523
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00523
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
73A Query on 73A Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	(2E)-3-[4-amino-5-(4-chlorophenyl)-7-(2-methoxyethyl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]-2-cyano-N-(propan-2-yl)prop-2-enamide C₂₂ H₂₃ Cl N₆ O₂ VJGVUTLADNGMJV-XNTDXEJSSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.323
R-Value Work: 0.264
R-Value Observed: 0.267
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.675	α = 102.08
b = 63.922	β = 90.36
c = 74.994	γ = 90.14

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-08-23

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM086858

Revision History (Full details and data files)

Version 1.0: 2017-08-23
Type: Initial release
Version 1.1: 2018-01-17
Changes: Author supporting evidence
Version 1.2: 2019-12-25
Changes: Author supporting evidence

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.