3KEC | pdb_00003kec

Crystal Structure of Human MMP-13 complexed with a phenyl-2H-tetrazole compound

PDB DOI: https://doi.org/10.2210/pdb3KEC/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-10-25 Released: 2010-11-10
Deposition Author(s): Shieh, H.-S., Pavlovsky, A.G., Collins, B., Schnute, M.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.204 (Depositor), 0.212 (DCC)
R-Value Work:
0.169 (Depositor), 0.175 (DCC)
R-Value Observed:
0.170 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery of (pyridin-4-yl)-2H-tetrazole as a novel scaffold to identify highly selective matrix metalloproteinase-13 inhibitors for the treatment of osteoarthritis.

Schnute, M.E., O'Brien, P.M., Nahra, J., Morris, M., Howard Roark, W., Hanau, C.E., Ruminski, P.G., Scholten, J.A., Fletcher, T.R., Hamper, B.C., Carroll, J.N., Patt, W.C., Shieh, H.S., Collins, B., Pavlovsky, A.G., Palmquist, K.E., Aston, K.W., Hitchcock, J., Rogers, M.D., McDonald, J., Johnson, A.R., Munie, G.E., Wittwer, A.J., Man, C.F., Settle, S.L., Nemirovskiy, O., Vickery, L.E., Agawal, A., Dyer, R.D., Sunyer, T.

(2010) Bioorg Med Chem Lett 20: 576-580

PubMed: 20005097 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2009.11.081
Primary Citation Related Structures:
3KEC, 3KEJ, 3KEK

PubMed Abstract:
Potent, highly selective and orally-bioavailable MMP-13 inhibitors have been identified based upon a (pyridin-4-yl)-2H-tetrazole scaffold. Co-crystal structure analysis revealed that the inhibitors bind at the S(1)(') active site pocket and are not ligands for the catalytic zinc atom. Compound 29b demonstrated reduction of cartilage degradation biomarker (TIINE) levels associated with cartilage protection in a preclinical rat osteoarthritis model.

Organizational Affiliation

Global Research and Development, Pfizer Inc., 700 Chesterfield Parkway West, St. Louis, MO 63017, USA. mark.e.schnute@pfizer.com

Macromolecule Content

Total Structure Weight: 39.29 kDa
Atom Count: 2,969
Modeled Residue Count: 334
Deposited Residue Count: 334
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	167	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P45452
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3KE Query on 3KE Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain J [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain J [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain J [auth A]	J [auth A], Q [auth B]	4-{[({3-[2-(4-methoxybenzyl)-2H-tetrazol-5-yl]phenyl}carbonyl)amino]methyl}benzoic acid C₂₄ H₂₁ N₅ O₄ VUTBCSIBPMXNCZ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain Q [auth B] Interactions & Density Focus chain J [auth A] Focus chain Q [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
HAE Query on HAE Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain R [auth B] MOL2 format, chain K [auth A] MOL2 format, chain R [auth B] mmCIF format, chain K [auth A] mmCIF format, chain R [auth B]	K [auth A], R [auth B]	ACETOHYDROXAMIC ACID C₂ H₅ N O₂ RRUDCFGSUDOHDG-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain R [auth B] Interactions & Density Focus chain K [auth A] Focus chain R [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], L [auth B], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth B] Focus chain M [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] N [auth B] O [auth B] E [auth A], F [auth A], G [auth A], N [auth B], O [auth B], P [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 N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.204 (Depositor), 0.212 (DCC)
R-Value Work: 0.169 (Depositor), 0.175 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.209	α = 90
b = 72.348	β = 90
c = 36.356	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-11-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-11-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations

3KEC | pdb_00003kec

Crystal Structure of Human MMP-13 complexed with a phenyl-2H-tetrazole compound

Literature

Discovery of (pyridin-4-yl)-2H-tetrazole as a novel scaffold to identify highly selective matrix metalloproteinase-13 inhibitors for the treatment of osteoarthritis.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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