SMTL ID : 2y6d.1

The Discovery of MMP7 Inhibitors Exploiting a Novel Selectivity Trigger

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 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.2: 5 residues within 4Å: Chain A: 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.2, H2O.3 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.9: 5 residues within 4Å: Chain B: 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.6, H2O.7 CA.15: 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.16: 5 residues within 4Å: Chain C: 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.10, H2O.11 CA.22: 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 CA.23: 5 residues within 4Å: Chain D: 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.14, H2O.15

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: TQJ.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.121, A:H.125, A:H.131 ZN.10: 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.11: 4 residues within 4Å: Chain B: H.121, H.125, H.131 Ligands: TQJ.14 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.121, B:H.125, B:H.131 ZN.17: 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.18: 4 residues within 4Å: Chain C: H.121, H.125, H.131 Ligands: TQJ.21 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.121, C:H.125, C:H.131 ZN.24: 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.25: 4 residues within 4Å: Chain D: H.121, H.125, H.131 Ligands: TQJ.28 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.121, D:H.125, D:H.131

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

SO4.5: 3 residues within 4Å: Chain A: P.28, H.29, I.30 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.29, A:I.30 Salt bridges: A:H.29 SO4.6: 3 residues within 4Å: Chain A: N.136, S.154, Q.155 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.136, A:Q.155, A:D.156 Water bridges: A:S.154 SO4.12: 3 residues within 4Å: Chain B: P.28, H.29, I.30 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.29, B:I.30 Salt bridges: B:H.29 SO4.13: 3 residues within 4Å: Chain B: N.136, S.154, Q.155 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.136, B:Q.155, B:D.156 Water bridges: B:S.154 SO4.19: 3 residues within 4Å: Chain C: P.28, H.29, I.30 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.29, C:I.30 Salt bridges: C:H.29 SO4.20: 3 residues within 4Å: Chain C: N.136, S.154, Q.155 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.136, C:Q.155, C:D.156 Water bridges: C:S.154 SO4.26: 3 residues within 4Å: Chain D: P.28, H.29, I.30 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.29, D:I.30 Salt bridges: D:H.29 SO4.27: 3 residues within 4Å: Chain D: N.136, S.154, Q.155 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.136, D:Q.155, D:D.156 Water bridges: D:S.154

4 x TQJ: N-[(2S)-1-[4-(5-BROMOPYRIDIN-2-YL)PIPERAZIN-1-YL]SULFONYL-5-PYRIMIDIN-2-YL-PENTAN-2-YL]-N-HYDROXY-METHANAMIDE(Non-covalent)

TQJ.7: 17 residues within 4Å: Chain A: Y.74, L.83, A.84, H.85, A.86, Y.117, A.118, H.121, E.122, H.125, H.131, V.138, Y.140, P.141, T.142, Y.143 Ligands: ZN.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.85, A:Y.143 Hydrogen bonds: A:A.84 Water bridges: A:A.86 Salt bridges: A:E.122 pi-Stacking: A:Y.74 TQJ.14: 17 residues within 4Å: Chain B: Y.74, L.83, A.84, H.85, A.86, Y.117, A.118, H.121, E.122, H.125, H.131, V.138, Y.140, P.141, T.142, Y.143 Ligands: ZN.11 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:H.85, B:Y.143 Hydrogen bonds: B:A.84 Water bridges: B:A.86 Salt bridges: B:E.122 pi-Stacking: B:Y.74 TQJ.21: 17 residues within 4Å: Chain C: Y.74, L.83, A.84, H.85, A.86, Y.117, A.118, H.121, E.122, H.125, H.131, V.138, Y.140, P.141, T.142, Y.143 Ligands: ZN.18 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:H.85, C:Y.143 Hydrogen bonds: C:A.84 Water bridges: C:A.86 Salt bridges: C:E.122 pi-Stacking: C:Y.74 TQJ.28: 17 residues within 4Å: Chain D: Y.74, L.83, A.84, H.85, A.86, Y.117, A.118, H.121, E.122, H.125, H.131, V.138, Y.140, P.141, T.142, Y.143 Ligands: ZN.25 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:H.85, D:Y.143 Hydrogen bonds: D:A.84 Water bridges: D:A.86 Salt bridges: D:E.122 pi-Stacking: D:Y.74

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