7JU8

X-ray structure of MMP-13 in Complex with 4-(1,2,3-thiadiazol-4-yl)pyridine

PDB DOI: https://doi.org/10.2210/pdb7JU8/pdb

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

Deposited: 2020-08-19 Released: 2021-08-04
Deposition Author(s): Farrow, N.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.264
R-Value Work: 0.198
R-Value Observed: 0.201

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Indole Inhibitors of MMP-13 for Arthritic Disorders

Taylor, S.J., Abeywardane, A., Liang, S., Xiong, Z., Proudfoot, J.R., Farmer, B.S., Gao, D.A., Heim-Riether, A., Smith-Keenan, L.L., Muegge, I., Yu, Y., Zhang, Q., Souza, D., Panzenbeck, M., Goldberg, D., Hill-Drzewi, M., Margarit, M., Collins, B., Li, J.X., Zuvela-Jelaska, L., Li, J., Farrow, N.A.

(2021) ACS Omega 6: 18635-18650

DOI: https://doi.org/10.1021/acsomega.1c01320

Macromolecule Content

Total Structure Weight: 40.07 kDa
Atom Count: 3,138
Modelled Residue Count: 333
Deposited Residue Count: 342
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagenase 3	A, B	171	Homo sapiens	Mutation(s): 0 Gene Names: MMP13 EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for P45452 (Homo sapiens) Explore P45452 Go to UniProtKB: P45452
PHAROS: P45452 GTEx: ENSG00000137745
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P45452
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain Y [auth B] MOL2 format, chain Y [auth B]	Y [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain Y [auth B] Interactions & Density Focus chain Y [auth B]
9DY (Subject of Investigation/LOI) Query on 9DY Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain S [auth B] MOL2 format, chain G [auth A] MOL2 format, chain S [auth B]	G [auth A], S [auth B]	4-(1,2,3-thiadiazol-4-yl)pyridine C₇ H₅ N₃ S CBBNSZNUEUONCU-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain S [auth B] Interactions & Density Focus chain G [auth A] Focus chain S [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A]	M [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B]	C [auth A], D [auth A], O [auth B], P [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain O [auth B] Focus chain P [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], N [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B]	E [auth A], F [auth A], Q [auth B], R [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain Q [auth B] Focus chain R [auth B]