2D1O

Stromelysin-1 (MMP-3) complexed to a hydroxamic acid inhibitor

PDB DOI: https://doi.org/10.2210/pdb2D1O/pdb

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

Deposited: 2005-08-30 Released: 2006-06-27
Deposition Author(s): Kohno, T., Hochigai, H., Yamashita, E., Tsukihara, T., Kanaoka, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.206
R-Value Work: 0.183
R-Value Observed: 0.183

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453

Kohno, T., Hochigai, H., Yamashita, E., Tsukihara, T., Kanaoka, M.

(2006) Biochem Biophys Res Commun 344: 315-322

PubMed: 16603129 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2006.03.098
Primary Citation of Related Structures:
2D1N, 2D1O

PubMed Abstract:
Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453 have been solved at 2.01 and 2.37A resolutions, respectively. The results revealed that the binding modes for this inhibitor to MMP-3 and -13 were quite similar. However, subtle comparative differences were observed at the bottom of S1' pockets, which were occupied with the guanidinomethyl moiety of the inhibitor. A remarkable feature of the inhibitor was the deep penetration of its long aliphatic chain into the S1' pocket and exposure of the guanidinomethyl moiety to the solvent.

Organizational Affiliation

Drug Research Division, Dainippon Sumitomo Pharma Co., Ltd., 3-1-98 Kasugadenaka, Konohana-ku, Osaka 554-0022, Japan. tetsuya-kono@ds-pharma.co.jp

Macromolecule Content

Total Structure Weight: 39.8 kDa
Atom Count: 2,979
Modelled Residue Count: 339
Deposited Residue Count: 342
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stromelysin-1	A, B	171	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
FA4 Query on FA4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B]	H [auth A], N [auth B]	SM-25453 C₂₄ H₄₂ N₆ O₃ DPKFTMHWVJEOMW-OAQYLSRUSA-N		Interactions Focus chain H [auth A] Focus chain N [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 I [auth B] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	C [auth A], D [auth A], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth B] Focus chain J [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 K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	E [auth A] F [auth A] G [auth A] K [auth B] L [auth B] E [auth A], F [auth A], G [auth A], K [auth B], L [auth B], M [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 K [auth B] Focus chain L [auth B] Focus chain M [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
FA4	PDBBind: 2D1O	Ki: 20 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.206
R-Value Work: 0.183
R-Value Observed: 0.183
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.36	α = 90
b = 50.95	β = 105
c = 80.79	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-06-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-06-27
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary