4MAN

Bcl_2-Navitoclax Analog (with Indole) Complex

PDB DOI: https://doi.org/10.2210/pdb4MAN/pdb
Entry: 4MAN supersedes: 4LXE

Classification: APOPTOSIS REGULATOR/INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-08-16 Released: 2014-01-29
Deposition Author(s): Park, C.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.234
R-Value Work: 0.213
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

ABT-199, a potent and selective BCL-2 inhibitor, achieves antitumor activity while sparing platelets.

Souers, A.J., Leverson, J.D., Boghaert, E.R., Ackler, S.L., Catron, N.D., Chen, J., Dayton, B.D., Ding, H., Enschede, S.H., Fairbrother, W.J., Huang, D.C., Hymowitz, S.G., Jin, S., Khaw, S.L., Kovar, P.J., Lam, L.T., Lee, J., Maecker, H.L., Marsh, K.C., Mason, K.D., Mitten, M.J., Nimmer, P.M., Oleksijew, A., Park, C.H., Park, C.M., Phillips, D.C., Roberts, A.W., Sampath, D., Seymour, J.F., Smith, M.L., Sullivan, G.M., Tahir, S.K., Tse, C., Wendt, M.D., Xiao, Y., Xue, J.C., Zhang, H., Humerickhouse, R.A., Rosenberg, S.H., Elmore, S.W.

(2013) Nat Med 19: 202-208

PubMed: 23291630 Search on PubMed
DOI: https://doi.org/10.1038/nm.3048
Primary Citation of Related Structures:
4LVT, 4LXD, 4MAN

PubMed Abstract:

Macromolecule Content

Total Structure Weight: 40.56 kDa
Atom Count: 2,656
Modelled Residue Count: 272
Deposited Residue Count: 332
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apoptosis regulator Bcl-2	A, B	166	Homo sapiens	Mutation(s): 0 Gene Names: BCL2
UniProt & NIH Common Fund Data Resources
Find proteins for P10415 (Homo sapiens) Explore P10415 Go to UniProtKB: P10415
PHAROS: P10415
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10415
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1Y1 Query on 1Y1 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]	4-[4-({4'-chloro-3-[2-(dimethylamino)ethoxy]biphenyl-2-yl}methyl)piperazin-1-yl]-2-(1H-indol-5-yloxy)-N-({3-nitro-4-[(tetrahydro-2H-pyran-4-ylmethyl)amino]phenyl}sulfonyl)benzamide C₄₈ H₅₂ Cl N₇ O₈ S OEPSXIVYHBPSCA-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.234
R-Value Work: 0.213
R-Value Observed: 0.214
Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.375	α = 90
b = 71.375	β = 90
c = 101.492	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
AMoRE	phasing
BUSTER	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-01-29

Deposition Author(s):

This entry supersedes: 4LXE

Revision History (Full details and data files)

Version 1.0: 2014-01-29
Type: Initial release
Version 1.1: 2017-08-02
Changes: Refinement description, Source and taxonomy
Version 1.2: 2017-11-15
Changes: Refinement description

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.