8X62 | pdb_00008x62

crystal structure of human Mcl-1 kinase domain in complex with RM1

PDB DOI: https://doi.org/10.2210/pdb8X62/pdb

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

Deposited: 2023-11-20 Released: 2025-05-21
Deposition Author(s): Zhang, Z.M., Wang, L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.288 (Depositor), 0.286 (DCC)
R-Value Work:
0.255 (Depositor), 0.258 (DCC)
R-Value Observed:
0.255 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

crystal structure of human Mcl-1 kinase domain in complex with RM1

Zhang, Z.M., Wang, L.

To be published.

Macromolecule Content

Total Structure Weight: 35.14 kDa
Atom Count: 2,248
Modeled Residue Count: 297
Deposited Residue Count: 302
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Induced myeloid leukemia cell differentiation protein Mcl-1	A, B	151	Homo sapiens	Mutation(s): 0 Gene Names: MCL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q07820 (Homo sapiens) Explore Q07820 Go to UniProtKB: Q07820
PHAROS: Q07820 GTEx: ENSG00000143384
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q07820
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YO0 (Subject of Investigation/LOI) Query on YO0 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1-[7-[1,5-dimethyl-3-(phenoxymethyl)pyrazol-4-yl]-3-(3-naphthalen-1-yloxypropyl)-1~{H}-indol-2-yl]-2,2-bis(oxidanyl)ethanone C₃₅ H₃₃ N₃ O₅ WZCPCAOYSVDSOO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.288 (Depositor), 0.286 (DCC)
R-Value Work: 0.255 (Depositor), 0.258 (DCC)
R-Value Observed: 0.255 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.761	α = 90
b = 56.011	β = 112.771
c = 66.097	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASES	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-05-21
Type: Initial release

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.