3TZ8

Kinase domain of cSrc in complex with RL104

PDB DOI: https://doi.org/10.2210/pdb3TZ8/pdb

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

Deposited: 2011-09-27 Released: 2012-10-10
Deposition Author(s): Gruetter, C., Richters, A., Rauh, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.258
R-Value Work: 0.198
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Overcoming Gatekeeper Mutations in cSrc and Abl by Hybrid Compound Design

Richters, A., Getlik, M., Gruetter, C., Schneider, R., Heuckmann, J.M., Heynck, S., Sos, M.L., Thomas, R.K., Rauh, D.

To be published.

Macromolecule Content

Total Structure Weight: 66.81 kDa
Atom Count: 4,373
Modelled Residue Count: 524
Deposited Residue Count: 572
Unique protein chains: 1

Macromolecules

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(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, v-Src sarcoma viral oncogene 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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AQM Query on AQM 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]	N-(4-{[4-({[1-(3-aminophenyl)-3-tert-butyl-1H-pyrazol-5-yl]carbamoyl}amino)phenyl]amino}quinazolin-6-yl)-3-(4-methylpiperazin-1-yl)propanamide C₃₆ H₄₃ N₁₁ O₂ SIXVDPYFTBZLMQ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
AQM	BindingDB: 3TZ8	IC50: 1.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.258
R-Value Work: 0.198
R-Value Observed: 0.200
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42	α = 79.08
b = 63.58	β = 87.69
c = 74.51	γ = 89.88

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SLS-Software	data collection
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-10-10

Deposition Author(s):

Gruetter, C.

Richters, A.

Rauh, D.

Revision History (Full details and data files)

Version 1.0: 2012-10-10
Type: Initial release
Version 1.1: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

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Deposit Data

Help and Resources

3TZ8

Kinase domain of cSrc in complex with RL104

Overcoming Gatekeeper Mutations in cSrc and Abl by Hybrid Compound Design

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)