SMTL ID : 8k4z.1

Crystal structure of human MMP-7 in complex with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x 7SF- GGL- GLY- N9P- TBG- PAB: Inhibitor(Non-covalent)

7SF-GGL-GLY-N9P-TBG-PAB.1: 22 residues within 4Å: Chain A: F.6, Y.75, T.83, L.84, A.85, H.86, A.87, F.88, A.89, T.92, G.93, L.94, G.95, Y.118, A.119, H.122, Q.123, H.126, H.132, P.142, Y.144 Ligands: ZN.5 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.6, A:F.88, A:L.94 Hydrogen bonds: A:L.84, A:A.85, A:A.85, A:A.87, A:A.87, A:A.89, A:T.92, A:L.94, A:Q.123 Water bridges: A:H.132, A:H.132 Salt bridges: A:H.122, A:H.126, A:H.132 pi-Stacking: A:Y.75, A:H.122 Halogen bonds: A:A.119

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.61, G.93, L.94, G.95, D.97 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.61, A:G.93, A:G.95, A:D.97, H2O.1, H2O.1 CA.3: 6 residues within 4Å: Chain A: D.78, G.79, G.81, T.83, D.101, E.104 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.78, A:G.79, A:G.81, A:T.83, A:D.101, A:E.104

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: H.71, D.73, H.86, H.99 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.71, A:D.73, A:H.86, A:H.99 ZN.5: 4 residues within 4Å: Chain A: H.122, H.126, H.132 Ligands: 7SF-GGL-GLY-N9P-TBG-PAB.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.122, A:H.126, A:H.132

1 x IOD: IODIDE ION(Non-functional Binders)

IOD.6: 3 residues within 4Å: Chain A: G.72, D.73, S.74 Ligand excluded by PLIP

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 2 residues within 4Å: Chain A: S.155, Q.156 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oka, Y. et al., Discovery of TP0628103: A Highly Potent and Selective MMP-7 Inhibitor with Reduced OATP-Mediated Clearance Designed by Shifting Isoelectric Points. J.Med.Chem. (2024)

Release Date

2024-04-17

Peptides

Matrilysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Matrilysin

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