7M2E | pdb_00007m2e

Crystal structure of BPTF bromodomain in complex with CB02-092

PDB DOI: https://doi.org/10.2210/pdb7M2E/pdb

Classification: GENE REGULATION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-03-16 Released: 2022-02-16
Deposition Author(s): Nithianantham, S., Fischer, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.215 (Depositor), 0.218 (DCC)
R-Value Work:
0.167 (Depositor), 0.169 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

New Design Rules for Developing Potent Cell-Active Inhibitors of the Nucleosome Remodeling Factor (NURF) via BPTF Bromodomain Inhibition

Zahid, H., Buchholz, C.R., Singh, M., Ciccone, M.F., Chan, A., Nithianantham, S., Shi, K., Aihara, H., Fischer, M., Schonbrunn, E., dos Santos, C.O., Landry, J.W., Pomerantz, W.C.K.

(2021) J Med Chem 64: 13902-13917

DOI: https://doi.org/10.1021/acs.jmedchem.1c01294

Macromolecule Content

Total Structure Weight: 14.76 kDa
Atom Count: 1,178
Modeled Residue Count: 120
Deposited Residue Count: 123
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleosome-remodeling factor subunit BPTF	A	123	Homo sapiens	Mutation(s): 0 Gene Names: BPTF, FAC1, FALZ
UniProt & NIH Common Fund Data Resources
Find proteins for Q12830 (Homo sapiens) Explore Q12830 Go to UniProtKB: Q12830
PHAROS: Q12830 GTEx: ENSG00000171634
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12830
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YOV (Subject of Investigation/LOI) Query on YOV Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-chloro-5-{4-[2-(dimethylamino)ethyl]anilino}-2-methylpyridazin-3(2H)-one C₁₅ H₁₉ Cl N₄ O GMOXVZIZCRBKJB-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
YOV	BindingDB: 7M2E	IC50: 170 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.215 (Depositor), 0.218 (DCC)
R-Value Work: 0.167 (Depositor), 0.169 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.006	α = 90
b = 66.546	β = 105.61
c = 39.623	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2022-02-16

Deposition Author(s):

Nithianantham, S.

Revision History (Full details and data files)

Version 1.0: 2022-02-16
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, 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.