1D8M

CRYSTAL STRUCTURE OF MMP3 COMPLEXED WITH A HETEROCYCLE-BASED INHIBITOR

PDB DOI: https://doi.org/10.2210/pdb1D8M/pdb

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

Deposited: 1999-10-25 Released: 2000-10-25
Deposition Author(s): Pikul, S., Dunham, K.M., Almstead, N.G., De, B., Natchus, M.G., Taiwo, Y.O., Williams, L.E., Hynd, B.A., Hsieh, L.C., Janusz, M.J., Gu, F., Mieling, G.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free: 0.315
R-Value Work: 0.277

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Heterocycle-based MMP inhibitors with P2' substituents.

Pikul, S., Dunham, K.M., Almstead, N.G., De, B., Natchus, M.G., Taiwo, Y.O., Williams, L.E., Hynd, B.A., Hsieh, L.C., Janusz, M.J., Gu, F., Mieling, G.E.

(2001) Bioorg Med Chem Lett 11: 1009-1013

PubMed: 11327577 Search on PubMed
DOI: https://doi.org/10.1016/s0960-894x(01)00137-8
Primary Citation of Related Structures:
1D8M, 1G05

PubMed Abstract:
Potent and selective inhibition of matrix metalloproteinases was demonstrated for a series of sulfonamide-based hydroxamic acids. The design of the heterocyclic sulfonamides incorporates a six- or seven-member central ring with a P2' substituent that can be modified. Binding interactions of this substituent at the S2' site are believed to contribute to high inhibitory potency against stromelysin, collagenase-3 and gelatinases A and B, and to provide selectivity against collagenase-1 and matrilysin. An X-ray structure of a stromelysin inhibitor complex was obtained to provide insights into the SAR and selectivity trends observed for the series.

Organizational Affiliation

Procter and Gamble Pharmaceuticals, Health Care Research Center, Mason, OH 45040, USA. spikul@avalonrx.com

Macromolecule Content

Total Structure Weight: 39.75 kDa
Atom Count: 2,831
Modelled Residue Count: 342
Deposited Residue Count: 346
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STROMELYSIN-1 PRECURSOR	A, B	173	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08254
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BBH Query on BBH Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	1-BENZYL-3-(4-METHOXY-BENZENESULFONYL)-6-OXO-HEXAHYDRO-PYRIMIDINE-4-CARBOXYLIC ACID HYDROXYAMIDE C₁₉ H₂₁ N₃ O₆ S SUSMVCKSLVPRCL-QGZVFWFLSA-N		Interactions Focus chain M [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	C [auth A], D [auth A], H [auth B], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [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 G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	E [auth A] F [auth A] G [auth A] J [auth B] K [auth B] E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
BBH	PDBBind: 1D8M	IC50: 3.1 (nM) from 1 assay(s)
BBH	BindingDB: 1D8M	IC50: 3.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free: 0.315
R-Value Work: 0.277
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.96	α = 90
b = 78.59	β = 90
c = 105.93	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2000-10-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2000-10-25
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-07
Changes: Data collection, Database references, Derived calculations