1BM6

SOLUTION STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN STROMELYSIN-1 COMPLEXED TO A POTENT NON-PEPTIDIC INHIBITOR, NMR, 20 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION, ENERGY MINIMIZATION 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of the catalytic domain of human stromelysin-1 complexed to a potent, nonpeptidic inhibitor.

Li, Y.C.Zhang, X.Melton, R.Ganu, V.Gonnella, N.C.

(1998) Biochemistry 37: 14048-14056

  • DOI: 10.1021/bi981328w

  • PubMed Abstract: 
  • The full three-dimensional structure of the catalytic domain of human stromelysin-1 (SCD) complexed to a novel and potent, nonpeptidic inhibitor has been determined by nuclear magnetic resonance spectroscopy (NMR). To accurately mimic assay condition ...

    The full three-dimensional structure of the catalytic domain of human stromelysin-1 (SCD) complexed to a novel and potent, nonpeptidic inhibitor has been determined by nuclear magnetic resonance spectroscopy (NMR). To accurately mimic assay conditions, the structure was obtained in Tris buffer at pH 6.8 and without the presence of organic solvent. The results showed that the major site of enzyme-inhibitor interaction occurs in the S1' pocket whereas portions of the inhibitor that occupy the shallow S2' and S1 pockets remained primarily solvent exposed. Because this relatively small inhibitor could not deeply penetrate stromelysin's long narrow hydrophobic S1' pocket, the enzyme was found to adopt a dramatic fold in the loop region spanning residues 221-231, allowing occupation of the solvent-accessible S1' channel by the enzyme itself. This remarkable conformational fold at the enzyme binding site resulted in constriction of the S1' loop region about the inhibitor. Examination of the tertiary structure of the stromelysin-inhibitor complex revealed few hydrogen-bonding or hydrophobic interactions between the inhibitor and enzyme that can contribute to overall binding energy; hence the resultant compact structure may in part account for the relatively high potency exhibited by this inhibitor.


    Related Citations: 
    • The NMR Structure of the Inhibited Catalytic Domain of Human Stromelysin-1
      Gooley, P.R.,O'Connell, J.F.,Marcy, A.I.,Cuca, G.C.,Salowe, S.P.,Bush, B.L.,Hermes, J.D.,Esser, C.K.,Hagmann, W.K.,Springer, J.P.,Johnson, B.A.
      (1994) Nat.Struct.Mol.Biol. 1: 111


    Organizational Affiliation

    Novartis Pharmaceuticals Corporation, Summit, New Jersey 07901, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
STROMELYSIN-1
A
173Homo sapiensMutation(s): 0 
Gene Names: MMP3 (STMY1)
EC: 3.4.24.17
Find proteins for P08254 (Homo sapiens)
Go to Gene View: MMP3
Go to UniProtKB:  P08254
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MSB
Query on MSB

Download SDF File 
Download CCD File 
A
1-METHYLOXY-4-SULFONE-BENZENE
C7 H8 O3 S
XUNSZADDFLWFOL-UHFFFAOYSA-N
 Ligand Interaction
HAV
Query on HAV

Download SDF File 
Download CCD File 
A
HYDROXYAMINOVALINE
C5 H12 N2 O2
USSBBYRBOWZYSB-SCSAIBSYSA-N
 Ligand Interaction
3MP
Query on 3MP

Download SDF File 
Download CCD File 
A
3-METHYLPYRIDINE
C6 H7 N
ITQTTZVARXURQS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION, ENERGY MINIMIZATION 
  • Olderado: 1BM6 Olderado
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-07-29
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance