2PJT | pdb_00002pjt

Crystal structure of the catalytic domain of MMP-13 complexed with WAY-344

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.270 (Depositor) 
  • R-Value Work: 
    0.212 (Depositor) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structure-based design of TACE selective inhibitors: manipulations in the S1'-S3' pocket.

Huang, A., Joseph-McCarthy, D., Lovering, F., Sun, L., Wang, W., Xu, W., Zhu, Y., Cui, J., Zhang, Y., Levin, J.I.

(2007) Bioorg Med Chem 15: 6170-6181

  • DOI: https://doi.org/10.1016/j.bmc.2007.06.031
  • Primary Citation of Related Structures:  
    2PJT

  • PubMed Abstract: 

    A series of beta-sulfonyl hydroxamate TACE inhibitors, bearing a butynylamino or a butynyloxy P1' group, was designed and synthesized. Of the compounds investigated, 22 has excellent potency against isolated TACE enzyme, shows good selectivity over MMP-2 and MMP-13, and oral activity in an in vivo mouse model of TNF-alpha production.

    • Organizational Affiliation: 

    Chemical and Screening Sciences, Wyeth Research, 200 CambridgePark Drive, Cambridge, MA 02140, USA. ahuang@wyeth.com


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Collagenase 3
A, B, C, D
165Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45452
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
347
Query on 347
Download Ideal Coordinates CCD File 
J [auth A],
O [auth B],
U [auth C],
Z [auth D]		TERT-BUTYL 4-({[4-(BUT-2-YN-1-YLAMINO)PHENYL]SULFONYL}METHYL)-4-[(HYDROXYAMINO)CARBONYL]PIPERIDINE-1-CARBOXYLATE
C22 H31 N3 O6 S
RXFCFGLSOUOCEA-UHFFFAOYSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
K [auth B]
L [auth B]
P [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
M [auth B]
N [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
347 BindingDB:  2PJT IC50: 860 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.270 (Depositor) 
  • R-Value Work:  0.212 (Depositor) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.352α = 90
b = 35.789β = 108.94
c = 139.405γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling
AMoREphasing

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: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description