1DTH

METALLOPROTEASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Batimastat, a potent matrix mealloproteinase inhibitor, exhibits an unexpected mode of binding.

Botos, I.Scapozza, L.Zhang, D.Liotta, L.A.Meyer, E.F.

(1996) Proc Natl Acad Sci U S A 93: 2749-2754

  • DOI: 10.1073/pnas.93.7.2749
  • Primary Citation of Related Structures:  
    1DTH

  • PubMed Abstract: 
  • Matrix metalloproteinase enzymes have been implicated in degenerative processes like tumor cell invasion, metastasis, and arthritis. Specific metalloproteinase inhibitors have been used to block tumor cell proliferation. We have examined the interaction of batimastat (BB-94) with a metalloproteinase [atrolysin C (Ht-d), EC 3 ...

    Matrix metalloproteinase enzymes have been implicated in degenerative processes like tumor cell invasion, metastasis, and arthritis. Specific metalloproteinase inhibitors have been used to block tumor cell proliferation. We have examined the interaction of batimastat (BB-94) with a metalloproteinase [atrolysin C (Ht-d), EC 3.4.24.42] active site at 2.0-angstroms resolution (R = 16.8%). The title structure exhibits an unexpected binding geometry, with the thiophene ring deeply inserted into the primary specificity site. This unprecedented binding geometry dramatizes the significance of the cavernous primary specificity site, pointing the way for the design of a new generation of potential antitumor drugs.


    Related Citations: 
    • Structural Interaction of Natural and Synthetic Inhibitors with the Venom Metalloproteinase, Atrolysin C (Form D)
      Zhang, D., Botos, I., Gomis-Ruth, F.X., Doll, R., Blood, C., Njoroge, F.G., Fox, J.W., Bode, W., Meyer, E.F.
      (1994) Proc Natl Acad Sci U S A 91: 8447

    Organizational Affiliation

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, 77843, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATROLYSIN CA, B203Crotalus atroxMutation(s): 0 
EC: 3.4.24.42
UniProt
Find proteins for P15167 (Crotalus atrox)
Explore P15167 
Go to UniProtKB:  P15167
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BAT (Subject of Investigation/LOI)
Query on BAT

Download Ideal Coordinates CCD File 
E [auth A], H [auth B]4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE
C23 H31 N3 O4 S2
XFILPEOLDIKJHX-QYZOEREBSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
DSX PDBBind:  1DTH IC50: 6 (nM) from 1 assay(s)
BAT Binding MOAD:  1DTH IC50: 6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.21α = 90
b = 97.21β = 90
c = 87.91γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-02-12
    Type: Initial release
  • Version 1.1: 2008-03-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance