SMTL ID : 6esm.1

Crystal structure of MMP9 in complex with inhibitor BE4.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.117, H.121, H.127 Ligands: B9Z.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.117, A:H.121, A:H.127 ZN.2: 4 residues within 4Å: Chain A: H.66, D.68, H.81, H.94 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.66, A:D.68, A:H.81, A:H.94

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 7 residues within 4Å: Chain A: D.73, G.74, K.75, D.76, L.78, D.96, E.99 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.73, A:G.74, A:D.76, A:L.78, A:D.96, A:E.99 CA.4: 4 residues within 4Å: Chain A: D.56, G.88, Q.90, D.92 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.56, A:G.88, A:Q.90, A:D.92, H2O.1, H2O.1 CA.5: 4 residues within 4Å: Chain A: S.20, D.22, D.97, E.99 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.97, A:D.97, A:E.99, H2O.6, H2O.7

1 x B9Z: (2~{S})-2-[2-[4-(4-methoxyphenyl)phenyl]sulfanylphenyl]pentanedioic acid(Non-covalent)

B9Z.6: 20 residues within 4Å: Chain A: G.77, L.78, L.79, A.80, H.81, V.114, H.117, Q.118, H.121, H.127, A.133, L.134, Y.136, P.137, M.138, Y.139, R.140, T.142 Ligands: ZN.1, PZE.7 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.78, A:H.81, A:V.114, A:V.114, A:H.117, A:L.134, A:Y.139 Hydrogen bonds: A:A.80, A:Q.118 Water bridges: A:R.140, A:R.140 Salt bridges: A:H.117, A:H.121, A:H.127 pi-Stacking: A:H.117

1 x PZE: piperazine(Non-covalent)

PZE.7: 5 residues within 4Å: Chain A: Y.70, H.81, A.82, F.83 Ligands: B9Z.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nuti, E. et al., Development of Thioaryl-Based Matrix Metalloproteinase-12 Inhibitors with Alternative Zinc-Binding Groups: Synthesis, Potentiometric, NMR, and Crystallographic Studies. J. Med. Chem. (2018)

Release Date

2018-05-16

Peptides

Matrix metalloproteinase-9,Matrix metalloproteinase-9: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Matrix metalloproteinase-9,Matrix metalloproteinase-9