3WV2

Crystal structure of the catalytic domain of MMP-13 complexed with N-(3-methoxybenzyl)-4-oxo-3,4-dihydroquinazoline-2-carboxamide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

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Literature

Thieno[2,3-d]pyrimidine-2-carboxamides bearing a carboxybenzene group at 5-position: Highly potent, selective, and orally available MMP-13 inhibitors interacting with the S1 binding site

Nara, H., Sato, K., Naito, T., Mototani, H., Oki, H., Yamamoto, Y., Kuno, H., Santou, T., Kanzaki, N., Terauchi, J., Uchikawa, O., Kori, M.

(2014) Bioorg Med Chem 

  • DOI: 10.1016/j.bmc.2014.07.025
  • Primary Citation of Related Structures:  
    3WV2, 3WV3

  • PubMed Abstract: 

    • On the basis of X-ray co-crystal structures of matrix metalloproteinase-13 (MMP-13) in complex with its inhibitors, our structure-based drug design (SBDD) strategy was directed to achieving high affinity through optimal protein-ligand interaction with the unique S1″ hydrophobic specificity pocket ...

    On the basis of X-ray co-crystal structures of matrix metalloproteinase-13 (MMP-13) in complex with its inhibitors, our structure-based drug design (SBDD) strategy was directed to achieving high affinity through optimal protein-ligand interaction with the unique S1″ hydrophobic specificity pocket. This report details the optimization of lead compound 44 to highly potent and selective MMP-13 inhibitors based on fused pyrimidine scaffolds represented by the thienopyrimidin-4-one 26c. Furthermore, we have examined the release of collagen fragments from bovine nasal cartilage in response to a combination of IL-1 and oncostatin M.

    Organizational Affiliation: 

    Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Collagenase 3A, B171Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WGG
Query on WGG
Download Ideal Coordinates CCD File 
H [auth A],
N [auth B]		N-(3-methoxybenzyl)-4-oxo-3,4-dihydroquinazoline-2-carboxamide
C17 H15 N3 O3
AARSEFXVCWMMKV-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
I [auth B],
J [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
K [auth B],
L [auth B]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
G [auth A],
M [auth B]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
WGG BindingDB:  3WV2 IC50: min: 5.6, max: 12 (nM) from 2 assay(s)
Binding MOAD:  3WV2 IC50: 12 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.53α = 90
b = 35.719β = 135.29
c = 94.762γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2014-05-12 
  • Released Date: 2014-09-24 
    • Deposition Author(s): Oki, H., Tanaka, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-24
    Type: Initial release