7LH7 | pdb_00007lh7

Crystal structure of BCL-XL in complex with a benzothiazole-based inhibitor

PDB DOI: https://doi.org/10.2210/pdb7LH7/pdb

Classification: APOPTOSIS
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-01-21 Released: 2021-06-23
Deposition Author(s): Judge, R.A., Tao, Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free:
0.199 (Depositor), 0.197 (DCC)
R-Value Work:
0.185 (Depositor), 0.184 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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Literature

Structure-Based Design of A-1293102, a Potent and Selective BCL-XL Inhibitor

Tao, Z.F., Wang, X., Chen, J., Ingram, J.P., Jin, S., Judge, R.A., Kovar, P.J., Park, C., Sun, C., Wakefield, B.D., Zhou, L., Zhang, H., Elmore, S.W., Phillips, D.C., Judd, A.S., Leverson, J.D., Souers, A.J.

(2021) Acs Medicinal Chemistry Letters 12: 1011-1016

DOI: https://doi.org/10.1021/acsmedchemlett.1c00162

Macromolecule Content

Total Structure Weight: 39.32 kDa
Atom Count: 2,776
Modeled Residue Count: 289
Deposited Residue Count: 334
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bcl-2-like protein 1	A, B	167	Homo sapiens	Mutation(s): 3 Gene Names: BCL2L1, BCL2L, BCLX
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens) Explore Q07817 Go to UniProtKB: Q07817
PHAROS: Q07817 GTEx: ENSG00000171552
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q07817
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XZM (Subject of Investigation/LOI) Query on XZM Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	N-(1,3-benzothiazol-2-yl)-2-(4-{[(4-{[(2R)-4-(morpholin-4-yl)-1-(phenylsulfanyl)butan-2-yl]amino}-3-[(trifluoromethyl)sulfonyl]phenyl)sulfonyl]carbamoyl}-1,3-thiazol-2-yl)-1,2,3,4-tetrahydroisoquinoline-8-carboxamide C₄₂ H₄₀ F₃ N₇ O₇ S₅ GSXZYBFDAFXVFZ-MUUNZHRXSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free: 0.199 (Depositor), 0.197 (DCC)
R-Value Work: 0.185 (Depositor), 0.184 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.86	α = 90
b = 88.91	β = 90
c = 151.46	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-06-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-06-23
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.