8F97

Compound 5 bound to procaspase-6

PDB DOI: https://doi.org/10.2210/pdb8F97/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: 2.32 Å
R-Value Free: 0.210
R-Value Work: 0.179
R-Value Observed: 0.180

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: 137.75 kDa
Atom Count: 8,603
Modelled Residue Count: 996
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XM6 (Subject of Investigation/LOI) Query on XM6 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth C]	E [auth A], J [auth C]	2-({[(2M)-[2,3'-bipyridin]-2'-yl]amino}methyl)-5-fluorophenol C₁₇ H₁₄ F N₃ O FIQJLLWADQSRDK-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain P [auth D] MOL2 format, chain P [auth D]	P [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain P [auth D] Interactions & Density Focus chain P [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D]	F [auth A] G [auth B] H [auth B] K [auth C] L [auth C] F [auth A], G [auth B], H [auth B], K [auth C], L [auth C], M [auth C], N [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain O [auth D] MOL2 format, chain O [auth D]	O [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain O [auth D] Interactions & Density Focus chain O [auth D]