SMTL ID : 2y6c.1

THE DISCOVERY OF MMP7 INHIBITORS EXPLOITING A NOVEL SELECTIVITY TRIGGER

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: A.59, D.60, G.92, L.93, G.94, D.96 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.60, A:G.92, A:G.94, A:D.96, H2O.36, H2O.52 CA.2: 6 residues within 4Å: Chain A: D.77, G.78, G.80, T.82, D.100, E.103 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.77, A:G.78, A:G.80, A:T.82, A:D.100, A:E.103 CA.7: 6 residues within 4Å: Chain B: A.59, D.60, G.92, L.93, G.94, D.96 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.60, B:G.92, B:G.94, B:D.96, H2O.126, H2O.142 CA.8: 6 residues within 4Å: Chain B: D.77, G.78, G.80, T.82, D.100, E.103 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:D.77, B:G.78, B:G.80, B:T.82, B:D.100, B:E.103 CA.13: 6 residues within 4Å: Chain C: A.59, D.60, G.92, L.93, G.94, D.96 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.60, C:G.92, C:G.94, C:D.96, H2O.216, H2O.232 CA.14: 6 residues within 4Å: Chain C: D.77, G.78, G.80, T.82, D.100, E.103 6 PLIP interactions: 6 interactions with chain C Metal complexes: C:D.77, C:G.78, C:G.80, C:T.82, C:D.100, C:E.103 CA.19: 6 residues within 4Å: Chain D: A.59, D.60, G.92, L.93, G.94, D.96 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.60, D:G.92, D:G.94, D:D.96, H2O.306, H2O.322 CA.20: 6 residues within 4Å: Chain D: D.77, G.78, G.80, T.82, D.100, E.103 6 PLIP interactions: 6 interactions with chain D Metal complexes: D:D.77, D:G.78, D:G.80, D:T.82, D:D.100, D:E.103

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.70, D.72, H.85, H.98 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.70, A:D.72, A:H.85, A:H.98 ZN.4: 4 residues within 4Å: Chain A: H.121, H.125, H.131 Ligands: TQI.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.121, A:H.125, A:H.131, TQI.6 ZN.9: 4 residues within 4Å: Chain B: H.70, D.72, H.85, H.98 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.70, B:D.72, B:H.85, B:H.98 ZN.10: 4 residues within 4Å: Chain B: H.121, H.125, H.131 Ligands: TQI.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.121, B:H.125, B:H.131, TQI.12 ZN.15: 4 residues within 4Å: Chain C: H.70, D.72, H.85, H.98 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.70, C:D.72, C:H.85, C:H.98 ZN.16: 4 residues within 4Å: Chain C: H.121, H.125, H.131 Ligands: TQI.18 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.121, C:H.125, C:H.131, TQI.18 ZN.21: 4 residues within 4Å: Chain D: H.70, D.72, H.85, H.98 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.70, D:D.72, D:H.85, D:H.98 ZN.22: 4 residues within 4Å: Chain D: H.121, H.125, H.131 Ligands: TQI.24 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:H.121, D:H.125, D:H.131, TQI.24

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 8 residues within 4Å: Chain A: A.69, H.70, G.71, D.72, P.75 Chain B: L.83, I.113, Y.143 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.70, A:G.71, A:D.72 Water bridges: A:Y.74 SO4.11: 8 residues within 4Å: Chain B: A.69, H.70, G.71, D.72, P.75 Chain D: L.83, I.113, Y.143 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.70, B:G.71, B:D.72 Water bridges: B:Y.74 SO4.17: 8 residues within 4Å: Chain A: L.83, I.113, Y.143 Chain C: A.69, H.70, G.71, D.72, P.75 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.70, C:G.71, C:D.72 Water bridges: C:Y.74 SO4.23: 8 residues within 4Å: Chain C: L.83, I.113, Y.143 Chain D: A.69, H.70, G.71, D.72, P.75 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.70, D:G.71, D:D.72 Water bridges: D:Y.74

4 x TQI: N-{[4-CHLORO-3-(TRIFLUOROMETHYL)PHENYL]SULFONYL}-L-TRYPTOPHAN(Non-covalent)

TQI.6: 15 residues within 4Å: Chain A: F.5, T.82, L.83, A.84, H.85, A.86, Y.117, A.118, H.121, E.122, H.125, H.131, P.141, Y.143 Ligands: ZN.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.5 Hydrogen bonds: A:L.83, A:A.84, A:A.86 Salt bridges: A:H.121, A:H.125, A:H.131 pi-Stacking: A:H.125, A:H.131 Halogen bonds: A:A.118 TQI.12: 15 residues within 4Å: Chain B: F.5, T.82, L.83, A.84, H.85, A.86, Y.117, A.118, H.121, E.122, H.125, H.131, P.141, Y.143 Ligands: ZN.10 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.5 Hydrogen bonds: B:L.83, B:A.84, B:A.86 Salt bridges: B:H.121, B:H.125, B:H.131 pi-Stacking: B:H.125, B:H.131 Halogen bonds: B:A.118 TQI.18: 15 residues within 4Å: Chain C: F.5, T.82, L.83, A.84, H.85, A.86, Y.117, A.118, H.121, E.122, H.125, H.131, P.141, Y.143 Ligands: ZN.16 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.5 Hydrogen bonds: C:L.83, C:A.84, C:A.86 Salt bridges: C:H.121, C:H.125, C:H.131 pi-Stacking: C:H.125, C:H.131 Halogen bonds: C:A.118 TQI.24: 15 residues within 4Å: Chain D: F.5, T.82, L.83, A.84, H.85, A.86, Y.117, A.118, H.121, E.122, H.125, H.131, P.141, Y.143 Ligands: ZN.22 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.5 Hydrogen bonds: D:L.83, D:A.84, D:A.86 Salt bridges: D:H.121, D:H.125, D:H.131 pi-Stacking: D:H.125, D:H.131 Halogen bonds: D:A.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Edman, K. et al., The Discovery of Mmp7 Inhibitors Exploiting a Novel Selectivity Trigger. Chemmedchem (2011)

Release Date

2011-05-04

Peptides

MATRILYSIN: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

MATRILYSIN