3KRY

Crystal structure of MMP-13 in complex with SC-78080

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


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


Literature

Orally-active MMP-1 sparing alpha-tetrahydropyranyl and alpha-piperidinyl sulfone matrix metalloproteinase (MMP) inhibitors with efficacy in cancer, arthritis, and cardiovascular disease

Becker, D.P., Barta, T.E., Bedell, L.J., Boehm, T.L., Bond, B.R., Carroll, J., Carron, C.P., Decrescenzo, G.A., Easton, A.M., Freskos, J.N., Funckes-Shippy, C.L., Heron, M., Hockerman, S., Howard, C.P., Kiefer, J.R., Li, M.H., Mathis, K.J., McDonald, J.J., Mehta, P.P., Munie, G.E., Sunyer, T., Swearingen, C.A., Villamil, C.I., Welsch, D., Williams, J.M., Yu, Y., Yao, J.

(2010) J Med Chem 53: 6653-6680

  • DOI: 10.1021/jm100669j
  • Primary Citation of Related Structures:  
    3KRY

  • PubMed Abstract: 

    • α-Sulfone-α-piperidine and α-tetrahydropyranyl hydroxamates were explored that are potent inhibitors of MMP's-2, -9, and -13 that spare MMP-1, with oral efficacy in inhibiting tumor growth in mice and left-ventricular hypertrophy in rats and in the bovine cartilage degradation ex vivo explant system ...

    α-Sulfone-α-piperidine and α-tetrahydropyranyl hydroxamates were explored that are potent inhibitors of MMP's-2, -9, and -13 that spare MMP-1, with oral efficacy in inhibiting tumor growth in mice and left-ventricular hypertrophy in rats and in the bovine cartilage degradation ex vivo explant system. α-Piperidine 19v (SC-78080/SD-2590) was selected for development toward the initial indication of cancer, while α-piperidine and α-tetrahydropyranyl hydroxamates 19w (SC-77964) and 9i (SC-77774), respectively, were identified as backup compounds.

    Organizational Affiliation: 

    Pfizer Research, 700 Chesterfield Village Parkway, St. Louis, Missouri 63198, USA. dbecke3@luc.edu



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Collagenase 3 A, B, C, D164Homo sapiensMutation(s): 0 
Gene Names: MMP13
EC: 3.4.24
Find proteins for P45452 (Homo sapiens)
Explore P45452 
Go to UniProtKB:  P45452
NIH Common Fund Data Resources
PHAROS:  P45452
GTEx:  ENSG00000137745
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3KR
Query on 3KR
Download Ideal Coordinates CCD File 
A, B, C, D
1-(2-methoxyethyl)-N-oxo-4-({4-[4-(trifluoromethoxy)phenoxy]phenyl}sulfonyl)piperidine-4-carboxamide
C22 H23 F3 N2 O7 S
JMZMOQBVAXNXIQ-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3KRKd:  0.10000000149011612   nM  Binding MOAD
3KRIC50 :  0.10000000149011612   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.317α = 92.42
b = 70.016β = 94.23
c = 69.094γ = 104.94
Software Package:
Software NamePurpose
MAR345data collection
X-PLORmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-06-24
    Changes: Data collection
  • Version 1.3: 2017-11-01
    Changes: Refinement description