1XUD | pdb_00001xud

Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor

PDB DOI: https://doi.org/10.2210/pdb1XUD/pdb

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

Deposited: 2004-10-26 Released: 2005-10-26
Deposition Author(s): Engel, C.K., Wendt, K.U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.203 (Depositor)
R-Value Work:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structural basis for the highly selective inhibition of MMP-13.

Engel, C.K., Pirard, B., Schimanski, S., Kirsch, R., Habermann, J., Klingler, O., Schlotte, V., Weithmann, K.U., Wendt, K.U.

(2005) Chem Biol 12: 181-189

PubMed: 15734640 Search on PubMed
DOI: https://doi.org/10.1016/j.chembiol.2005.01.008
Primary Citation Related Structures:
1XUD, 1XUR

PubMed Abstract:
The paradigm for matrix metalloprotease inhibition combines active site tailoring and catalytic zinc ligation. But, selectivity has been difficult. Now, Engel et al. present novel compounds, completely selective for MMP-13, with a unique binding mode.

Organizational Affiliation

Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880, USA

Macromolecule Content

Total Structure Weight: 39.71 kDa
Atom Count: 3,208
Modeled Residue Count: 335
Deposited Residue Count: 342
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagenase 3	A, B	171	Homo sapiens	Mutation(s): 0 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P45452
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PB4 Query on PB4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	G [auth A], L [auth B]	N,N'-BIS(4-FLUORO-3-METHYLBENZYL)PYRIMIDINE-4,6-DICARBOXAMIDE C₂₂ H₂₀ F₂ N₄ O₂ PYFRREJCFXFNRR-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	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 J [auth B] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	E [auth A], F [auth A], J [auth B], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
PB4	BindingDB: 1XUD	IC50: min: 0.67, max: 110 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.203 (Depositor)
R-Value Work: 0.168 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.022	α = 90
b = 36.475	β = 130.412
c = 95.06	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
CNS	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-10-26

Deposition Author(s):

Engel, C.K.

Wendt, K.U.

Revision History (Full details and data files)

Version 1.0: 2005-10-26
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: 2024-03-13
Changes: Data collection, Database references, Derived calculations