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
  • Structures With Same Primary Citation

  • 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 b ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Collagenase 3A, 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3KR
Query on 3KR

Download 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 CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download 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



Entry History 

Deposition Data

Revision History 

  • 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