8F9C

Compound 20 bound to procaspase-6

PDB DOI: https://doi.org/10.2210/pdb8F9C/pdb

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

Deposited: 2022-11-23 Released: 2023-12-13
Deposition Author(s): Fan, P., Zhao, Y., Renslo, A.R., Arkin, M.R.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.231
R-Value Work: 0.193
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A Comprehensive Empirical-Computational Study of Diverse Heteroarene Stacking Interactions Under Physiological Conditions

Fan, P., Zhao, Y., Renslo, A.R., Arkin, M.R.

To be published.

Macromolecule Content

Total Structure Weight: 137.06 kDa
Atom Count: 8,137
Modelled Residue Count: 981
Deposited Residue Count: 1,196
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Procaspase-6	A, B, C, D	299	Homo sapiens	Mutation(s): 0 Gene Names: CASP6, MCH2 EC: 3.4.22.59
UniProt & NIH Common Fund Data Resources
Find proteins for P55212 (Homo sapiens) Explore P55212 Go to UniProtKB: P55212
PHAROS: P55212 GTEx: ENSG00000138794
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P55212
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XN9 (Subject of Investigation/LOI) Query on XN9 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth C]	E [auth A], F [auth C]	5-fluoro-2-({[(3M)-3-(4H-1,2,4-triazol-3-yl)pyridin-2-yl]amino}methyl)phenol C₁₄ H₁₂ F N₅ O QRRUXNVQGIXBIR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.231
R-Value Work: 0.193
R-Value Observed: 0.195
Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.423	α = 90
b = 101.423	β = 90
c = 321.949	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-12-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-12-13
Type: Initial release

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.