SMTL ID : 1usn.2 (2 other biounits)

CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN FIBROBLAST STROMELYSIN-1 INHIBITED WITH THIADIAZOLE INHIBITOR PNU-142372

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.119, H.123, H.129 Ligands: IN9.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.119, A:H.123, A:H.129 ZN.2: 4 residues within 4Å: Chain A: H.69, D.71, H.84, H.97 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.69, A:D.71, A:H.84, A:H.97 ZN.6: 5 residues within 4Å: Chain A: H.14 Chain B: H.14 Chain C: H.14 Ligands: ZN.13, ZN.20 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: B:H.14, A:H.14, C:H.14, H2O.5, H2O.9 ZN.8: 4 residues within 4Å: Chain B: H.119, H.123, H.129 Ligands: IN9.14 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.119, B:H.123, B:H.129 ZN.9: 4 residues within 4Å: Chain B: H.69, D.71, H.84, H.97 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.69, B:D.71, B:H.84, B:H.97 ZN.13: 5 residues within 4Å: Chain A: H.14 Chain B: H.14 Chain C: H.14 Ligands: ZN.6, ZN.20 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: B:H.14, A:H.14, C:H.14, H2O.1, H2O.9 ZN.15: 4 residues within 4Å: Chain C: H.119, H.123, H.129 Ligands: IN9.21 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.119, C:H.123, C:H.129 ZN.16: 4 residues within 4Å: Chain C: H.69, D.71, H.84, H.97 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.69, C:D.71, C:H.84, C:H.97 ZN.20: 5 residues within 4Å: Chain A: H.14 Chain B: H.14 Chain C: H.14 Ligands: ZN.6, ZN.13 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: B:H.14, A:H.14, C:H.14, H2O.1, H2O.5

9 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.76, G.77, G.79, V.81, D.99, E.102 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.76, A:G.77, A:G.79, A:V.81, A:D.99, A:E.102 CA.4: 4 residues within 4Å: Chain A: D.59, G.91, N.93, D.95 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.59, A:G.91, A:N.93, A:D.95, H2O.1, H2O.1 CA.5: 3 residues within 4Å: Chain A: D.25, D.100, E.102 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.25, A:D.100, A:D.100, A:E.102, H2O.1 CA.10: 6 residues within 4Å: Chain B: D.76, G.77, G.79, V.81, D.99, E.102 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:D.76, B:G.77, B:G.79, B:V.81, B:D.99, B:E.102 CA.11: 4 residues within 4Å: Chain B: D.59, G.91, N.93, D.95 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.59, B:G.91, B:N.93, B:D.95, H2O.5, H2O.5 CA.12: 3 residues within 4Å: Chain B: D.25, D.100, E.102 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.25, B:D.100, B:D.100, B:E.102, H2O.6 CA.17: 6 residues within 4Å: Chain C: D.76, G.77, G.79, V.81, D.99, E.102 6 PLIP interactions: 6 interactions with chain C Metal complexes: C:D.76, C:G.77, C:G.79, C:V.81, C:D.99, C:E.102 CA.18: 4 residues within 4Å: Chain C: D.59, G.91, N.93, D.95 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.59, C:G.91, C:N.93, C:D.95, H2O.9, H2O.10 CA.19: 3 residues within 4Å: Chain C: D.25, D.100, E.102 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.25, C:D.100, C:D.100, C:E.102, H2O.10

3 x IN9: 2-[3-(5-MERCAPTO-[1,3,4]THIADIAZOL-2YL)-UREIDO]-N-METHYL-3-PENTAFLUOROPHENYL-PROPIONAMIDE(Non-covalent)

IN9.7: 12 residues within 4Å: Chain A: F.4, Y.73, A.83, H.84, A.85, Y.86, A.87, H.119, E.120, H.123, H.129 Ligands: ZN.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.85, A:A.85, A:A.85, A:A.87 pi-Stacking: A:Y.73 pi-Cation interactions: A:H.123 IN9.14: 12 residues within 4Å: Chain B: F.4, Y.73, A.83, H.84, A.85, Y.86, A.87, H.119, E.120, H.123, H.129 Ligands: ZN.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.85, B:A.85, B:A.85, B:A.87 pi-Stacking: B:Y.73 pi-Cation interactions: B:H.123 IN9.21: 12 residues within 4Å: Chain C: F.4, Y.73, A.83, H.84, A.85, Y.86, A.87, H.119, E.120, H.123, H.129 Ligands: ZN.15 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:A.85, C:A.85, C:A.85, C:A.87 pi-Stacking: C:Y.73 pi-Cation interactions: C:H.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Finzel, B.C. et al., Structural characterizations of nonpeptidic thiadiazole inhibitors of matrix metalloproteinases reveal the basis for stromelysin selectivity. Protein Sci. (1998)

Release Date

1998-12-23

Peptides

STROMELYSIN-1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

STROMELYSIN-1

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