SMTL ID : 4wzv.2 (1 other biounit)

Crystal structure of a hydroxamate based inhibitor EN140 in complex with the MMP-9 catalytic domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x E40: (2R)-4-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)-N-hydroxy-2-{[(4'-methoxybiphenyl-4-yl)sulfonyl](propan-2-yloxy)amino}butanamide(Non-covalent)

E40.1: 19 residues within 4Å: Chain A: G.77, L.78, L.79, A.80, H.81, A.82, L.113, V.114, H.117, E.118, H.121, D.126, H.127, L.134, Y.136, P.137, M.138, Y.139 Ligands: ZN.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.78, A:H.117, A:H.121, A:P.137, A:Y.139 Hydrogen bonds: A:L.79, A:A.80, A:A.80, A:A.82 pi-Stacking: A:H.117, A:H.121, A:H.121

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.117, H.121, H.127 Ligands: E40.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.117, A:H.121, A:H.127 ZN.3: 5 residues within 4Å: Chain A: H.66, D.68, Y.70, 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.4: 5 residues within 4Å: Chain A: A.55, 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.6, H2O.6 CA.5: 3 residues within 4Å: Chain A: D.22, D.97, E.99 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.22, A:D.97, A:D.97, A:E.99, H2O.3 CA.6: 6 residues within 4Å: Chain A: D.73, G.74, 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

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 1 residues within 4Å: Chain A: Y.51 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.51

1 x AZI: AZIDE ION(Non-functional Binders)

AZI.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

7 x NA: SODIUM ION(Non-functional Binders)

NA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.10: 1 residues within 4Å: Ligands: PEG.17 No protein-ligand interaction detected (PLIP) NA.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.12: 1 residues within 4Å: Chain A: R.49 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.49 Water bridges: A:D.29, A:D.29 NA.13: 1 residues within 4Å: Chain A: S.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.129 Water bridges: A:S.129 NA.14: 1 residues within 4Å: Chain A: G.160 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.160 NA.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.16: 4 residues within 4Å: Chain A: E.132, P.145, L.147, H.148 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.145

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.17: 1 residues within 4Å: Ligands: NA.10 No protein-ligand interaction detected (PLIP) PEG.18: 1 residues within 4Å: Chain A: G.69 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nuti, E. et al., N-O-Isopropyl Sulfonamido-Based Hydroxamates as Matrix Metalloproteinase Inhibitors: Hit Selection and in Vivo Antiangiogenic Activity. J.Med.Chem. (2015)

Release Date

2015-08-26

Peptides

Matrix metalloproteinase-9,Matrix metalloproteinase-9: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Matrix metalloproteinase-9,Matrix metalloproteinase-9

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