4DD8

ADAM-8 metalloproteinase domain with bound batimastat


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of human ADAM-8 catalytic domain complexed with batimastat.

Hall, T.Shieh, H.S.Day, J.E.Caspers, N.Chrencik, J.E.Williams, J.M.Pegg, L.E.Pauley, A.M.Moon, A.F.Krahn, J.M.Fischer, D.H.Kiefer, J.R.Tomasselli, A.G.Zack, M.D.

(2012) Acta Crystallogr.,Sect.F 68: 616-621

  • DOI: 10.1107/S1744309112015618

  • PubMed Abstract: 
  • The role of ADAM-8 in cancer and inflammatory diseases such as allergy, arthritis and asthma makes it an attractive target for drug development. Therefore, the catalytic domain of human ADAM-8 was expressed, purified and crystallized in complex with ...

    The role of ADAM-8 in cancer and inflammatory diseases such as allergy, arthritis and asthma makes it an attractive target for drug development. Therefore, the catalytic domain of human ADAM-8 was expressed, purified and crystallized in complex with a hydroxamic acid inhibitor, batimastat. The crystal structure of the enzyme-inhibitor complex was refined to 2.1 Å resolution. ADAM-8 has an overall fold similar to those of other ADAM members, including a central five-stranded β-sheet and a catalytic Zn(2+) ion. However, unique differences within the S1' binding loop of ADAM-8 are observed which might be exploited to confer specificity and selectivity to ADAM-8 competitive inhibitors for the treatment of diseases involving this enzyme.


    Organizational Affiliation

    Pfizer Inc, 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Disintegrin and metalloproteinase domain-containing protein 8
A, B, C, D
208Homo sapiensMutation(s): 0 
Gene Names: ADAM8 (MS2)
EC: 3.4.24.-
Find proteins for P78325 (Homo sapiens)
Go to Gene View: ADAM8
Go to UniProtKB:  P78325
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BAT
Query on BAT

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Download CCD File 
A, B, C, D
4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE
BATIMASTAT; BB94
C23 H31 N3 O4 S2
XFILPEOLDIKJHX-QYZOEREBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 91.600α = 90.00
b = 50.900β = 102.40
c = 93.500γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing
ADSCdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2012-06-27
    Type: Database references