4QNQ | pdb_00004qnq

Crystal Structure Analysis of full-length Bcl-XL in complex with the inhibitor ABT-263

PDB DOI: https://doi.org/10.2210/pdb4QNQ/pdb

Classification: APOPTOSIS/APOPTOSIS inhibitor
Organism(s): Rattus norvegicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-06-18 Released: 2015-10-28
Deposition Author(s): Korste, A., Vetter, I.R., Stoll, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.253 (Depositor), 0.258 (DCC)
R-Value Work:
0.206 (Depositor), 0.211 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure Analysis of full-length Bcl-XL in complex with the inhibitor ABT-263

Korste, A., Vetter, I.R., Stoll, R.

To be published.

Macromolecule Content

Total Structure Weight: 333.95 kDa
Atom Count: 14,929
Modeled Residue Count: 1,733
Deposited Residue Count: 2,880
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bcl-2-like protein 1	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	240	Rattus norvegicus	Mutation(s): 0 Gene Names: B2CL1_RAT, Bcl2l1, Bclx, Blc2l
UniProt
Find proteins for P53563 (Rattus norvegicus) Explore P53563 Go to UniProtKB: P53563
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53563
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1XJ Query on 1XJ Download:Ideal Coordinates CCD File SDF format, chain X [auth L] SDF format, chain W [auth K] SDF format, chain V [auth J] SDF format, chain U [auth I] SDF format, chain T [auth H] SDF format, chain S [auth G] SDF format, chain R [auth F] SDF format, chain Q [auth E] SDF format, chain P [auth D] SDF format, chain O [auth C] SDF format, chain N [auth B] SDF format, chain M [auth A] MOL2 format, chain X [auth L] MOL2 format, chain W [auth K] MOL2 format, chain V [auth J] MOL2 format, chain U [auth I] MOL2 format, chain T [auth H] MOL2 format, chain S [auth G] MOL2 format, chain R [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth A] mmCIF format, chain X [auth L] mmCIF format, chain W [auth K] mmCIF format, chain V [auth J] mmCIF format, chain U [auth I] mmCIF format, chain T [auth H] mmCIF format, chain S [auth G] mmCIF format, chain R [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain P [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth A]	M [auth A] N [auth B] O [auth C] P [auth D] Q [auth E] M [auth A], N [auth B], O [auth C], P [auth D], Q [auth E], R [auth F], S [auth G], T [auth H], U [auth I], V [auth J], W [auth K], X [auth L]	4-(4-{[2-(4-chlorophenyl)-5,5-dimethylcyclohex-1-en-1-yl]methyl}piperazin-1-yl)-N-[(4-{[(2R)-4-(morpholin-4-yl)-1-(phenylsulfanyl)butan-2-yl]amino}-3-[(trifluoromethyl)sulfonyl]phenyl)sulfonyl]benzamide C₄₇ H₅₅ Cl F₃ N₅ O₆ S₃ JLYAXFNOILIKPP-KXQOOQHDSA-N		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth K] Focus chain X [auth L] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth K] Focus chain X [auth L]

Binding Affinity Annotations
ID	Source	Binding Affinity
1XJ	BindingDB: 4QNQ	Ki: min: 0.05, max: 48 (nM) from 6 assay(s)
		Kd: min: 2.1, max: 55 (nM) from 2 assay(s)
		IC50: min: 8, max: 60 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.253 (Depositor), 0.258 (DCC)
R-Value Work: 0.206 (Depositor), 0.211 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.14	α = 72.94
b = 85.81	β = 67.42
c = 93.64	γ = 69.38

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DA+	data collection
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-10-28

Deposition Author(s):

Korste, A.

Vetter, I.R.

Stoll, R.

Revision History (Full details and data files)

Version 1.0: 2015-10-28
Type: Initial release
Version 1.1: 2017-08-23
Changes: Data collection
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description