SMTL ID : 8k5y.2 (1 other biounit)

Crystal structure of human proMMP-9 catalytic domain in complex with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.72, H.199, H.203, H.209 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.72, A:H.199, A:H.203, A:H.209 ZN.2: 4 residues within 4Å: Chain A: H.148, D.150, H.163, H.176 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.148, A:D.150, A:H.163, A:H.176

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.155, G.156, D.158, L.160, D.178, E.181 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.155, A:G.156, A:D.158, A:L.160, A:D.178, A:E.181 CA.4: 4 residues within 4Å: Chain A: S.102, D.104, D.179, E.181 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.104, A:D.179, A:D.179, A:E.181 CA.5: 4 residues within 4Å: Chain A: D.138, G.170, Q.172, D.174 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.138, A:G.170, A:Q.172, A:D.174, H2O.1, H2O.1

1 x VP6: (3-azanyl-4-fluoranyl-5,7,8,9-tetrahydropyrido[4,3-c]azepin-6-yl)-[6-(2-oxidanylpropan-2-yl)-1H-indol-2-yl]methanone(Non-covalent)

VP6.6: 17 residues within 4Å: Chain A: G.73, V.74, P.75, R.79, F.80, Q.81, F.83, L.87, Y.152, H.163, A.164, F.165, P.166, H.203, G.206, L.207, D.208 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.74, A:L.87, A:Y.152, A:P.166, A:P.166, A:D.208 Hydrogen bonds: A:R.79, A:Q.81, A:G.206 Water bridges: A:R.24, A:Q.81 pi-Stacking: A:Y.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishikawa-Shimono, R. et al., Discovery of novel indole derivatives as potent and selective inhibitors of proMMP-9 activation. Bioorg.Med.Chem.Lett. (2023)

Release Date

2023-12-06

Peptides

Matrix metalloproteinase-9: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Matrix metalloproteinase-9

Related Entries With Identical Sequence