SMTL ID : 1hfs.1

CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN FIBROBLAST STROMELYSIN-1 INHIBITED WITH THE N-CARBOXY-ALKYL INHIBITOR L-764,004

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.114, H.118, H.124 Ligands: L04.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.114, A:H.118, A:H.124 ZN.2: 5 residues within 4Å: Chain A: H.64, D.66, H.79, Y.81, H.92 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.64, A:D.66, A:H.79, A:H.92 ZN.7: 4 residues within 4Å: Chain B: H.114, H.118, H.124 Ligands: L04.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.114, B:H.118, B:H.124 ZN.8: 5 residues within 4Å: Chain B: H.64, D.66, H.79, Y.81, H.92 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.64, B:D.66, B:H.79, B:H.92

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.71, G.72, G.74, V.76, D.94, E.97 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.71, A:G.72, A:G.74, A:V.76, A:D.94, A:E.97 CA.4: 4 residues within 4Å: Chain A: D.54, G.86, N.88, D.90 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.54, A:G.86, A:N.88, A:D.90, H2O.1, H2O.1 CA.5: 3 residues within 4Å: Chain A: D.20, D.95, E.97 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.20, A:D.95, A:D.95, H2O.1, H2O.2 CA.9: 6 residues within 4Å: Chain B: D.71, G.72, G.74, V.76, D.94, E.97 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:D.71, B:G.72, B:G.74, B:V.76, B:D.94, B:E.97 CA.10: 4 residues within 4Å: Chain B: D.54, G.86, N.88, D.90 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.54, B:G.86, B:N.88, B:D.90, H2O.6, H2O.6 CA.11: 3 residues within 4Å: Chain B: D.20, D.95, E.97 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.20, B:D.95, B:D.95, H2O.6, H2O.7

2 x L04: 6-(4'-FLUORO-BIPHENYL-4-YL)-4-(3-METHYL-1-PHENYLCARBAMOYL-BUTYLCARBAMOYL)-2-[4-(1-OXO-1,3-DIHYDRO-ISOINDOL-2-YL)-BUTYL]-HEXANOIC ACID(Non-covalent)

L04.6: 29 residues within 4Å: Chain A: Y.68, N.75, V.76, L.77, A.78, H.79, A.80, Y.81, L.110, V.111, H.114, E.115, H.118, H.124, A.130, L.131, Y.133, P.134, L.135, Y.136, H.137, L.139 Chain B: F.123, H.124, S.125, A.126, Y.133, P.134 Ligands: ZN.1 24 PLIP interactions: 19 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.68, A:L.77, A:H.79, A:Y.81, A:L.110, A:H.114, A:L.131, A:Y.136, A:Y.136, A:Y.136, B:A.126, B:Y.133, B:P.134 Hydrogen bonds: A:N.75, A:L.77, A:P.134, A:Y.136 Salt bridges: A:H.114, A:H.118, A:H.124 pi-Stacking: A:Y.68, A:H.137, B:F.123, B:F.123 L04.12: 29 residues within 4Å: Chain A: F.123, H.124, S.125, A.126, Y.133, P.134 Chain B: Y.68, N.75, V.76, L.77, A.78, H.79, A.80, Y.81, L.110, V.111, H.114, E.115, H.118, H.124, A.130, L.131, Y.133, P.134, L.135, Y.136, H.137, L.139 Ligands: ZN.7 24 PLIP interactions: 5 interactions with chain A, 19 interactions with chain B Hydrophobic interactions: A:A.126, A:Y.133, A:P.134, B:Y.68, B:L.77, B:H.79, B:Y.81, B:L.110, B:H.114, B:L.131, B:Y.136, B:Y.136, B:Y.136 pi-Stacking: A:F.123, A:F.123, B:Y.68, B:H.137 Hydrogen bonds: B:N.75, B:L.77, B:P.134, B:Y.136 Salt bridges: B:H.114, B:H.118, B:H.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Esser, C.K. et al., Inhibition of stromelysin-1 (MMP-3) by P1'-biphenylylethyl carboxyalkyl dipeptides. J.Med.Chem. (1997)

Release Date

1998-02-18

Peptides

STROMELYSIN-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

STROMELYSIN-1