1G4K | pdb_00001g4k

X-ray Structure of a Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin

PDB DOI: https://doi.org/10.2210/pdb1G4K/pdb

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

Deposited: 2000-10-27 Released: 2001-04-25
Deposition Author(s): Dunten, P., Kammlott, U., Crowther, R., Levin, W., Foley, L.H., Wang, P., Palermo, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.284 (Depositor)
R-Value Work:
0.244 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

X-ray structure of a novel matrix metalloproteinase inhibitor complexed to stromelysin.

Dunten, P., Kammlott, U., Crowther, R., Levin, W., Foley, L.H., Wang, P., Palermo, R.

(2001) Protein Sci 10: 923-926

PubMed: 11316871 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1110/ps.48401
Primary Citation Related Structures:
1G4K

PubMed Abstract:
A new class of matrix metalloproteinase (MMP) inhibitors has been identified by screening a collection of compounds against stromelysin. The inhibitors, 2,4,6-pyrimidine triones, have proven to be potent inhibitors of gelatinases A and B. An X-ray crystal structure of one representative compound bound to the catalytic domain of stromelysin shows that the compounds bind at the active site and ligand the active-site zinc. The pyrimidine triones mimic substrates in forming hydrogen bonds to key residues in the active site, and provide opportunities for placing appropriately chosen groups into the S1' specificity pocket of MMPS: A number of compounds have been synthesized and assayed against stromelysin, and the variations in potency are explained in terms of the binding mode revealed in the X-ray crystal structure.

Organizational Affiliation

Roche Research Center, Hoffmann-La Roche Inc., Nutley, New Jersey 07110, USA. pete.dunten@roche.com

Macromolecule Content

Total Structure Weight: 58.44 kDa
Atom Count: 4,294
Modeled Residue Count: 504
Deposited Residue Count: 504
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STROMELYSIN-1	A, B, C	168	Homo sapiens	Mutation(s): 0 EC: 3.4.24.17
UniProt & NIH Common Fund Data Resources
Find proteins for P08254 (Homo sapiens) Explore P08254 Go to UniProtKB: P08254
PHAROS: P08254 GTEx: ENSG00000149968
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08254
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HQQ Query on HQQ Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain V [auth C] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain V [auth C] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain V [auth C]	I [auth A], O [auth B], V [auth C]	5-METHYL-5-(4-PHENOXY-PHENYL)-PYRIMIDINE-2,4,6-TRIONE C₁₇ H₁₄ N₂ O₄ RTBMLCLTYAPKIF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Focus chain V [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain P [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	D [auth A] E [auth A] J [auth B] K [auth B] Q [auth C] D [auth A], E [auth A], J [auth B], K [auth B], Q [auth C], R [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain Q [auth C] Focus chain R [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C]	F [auth A] G [auth A] H [auth A] L [auth B] M [auth B] F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B], S [auth C], T [auth C], U [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
HQQ	BindingDB: 1G4K	IC50: 2000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.284 (Depositor)
R-Value Work: 0.244 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.8	α = 90
b = 103.8	β = 90
c = 147.49	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2001-04-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2001-04-25
Type: Initial release
Version 1.1: 2007-10-16
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2018-07-18
Changes: Data collection, Database references
Version 1.4: 2024-02-07
Changes: Data collection, Database references, Derived calculations