SMTL ID : 4xct.1

Crystal structure of a hydroxamate based inhibitor ARP101 (EN73) in complex with the MMP-9 catalytic domain.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x N73: (2~{R})-3-methyl-~{N}-oxidanylidene-2-[(4-phenylphenyl)sulfonyl-propan-2-yloxy-amino]butanamide(Non-covalent)

N73.1: 19 residues within 4Å: Chain A: G.74, L.75, L.76, A.77, H.78, L.110, V.111, H.114, E.115, H.118, H.124, L.131, Y.133, P.134, M.135, Y.136 Ligands: ZN.2, EDO.12, PGO.15 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.75, A:V.111, A:H.114, A:L.131, A:Y.136 Hydrogen bonds: A:A.77 pi-Stacking: A:H.114

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.114, H.118, H.124 Ligands: N73.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.114, A:H.118, A:H.124 ZN.3: 4 residues within 4Å: Chain A: H.63, D.65, H.78, H.91 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.63, A:D.65, A:H.78, A:H.91

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: D.70, G.71, D.73, L.75, D.93, E.96 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.70, A:G.71, A:D.73, A:L.75, A:D.93, A:E.96 CA.5: 4 residues within 4Å: Chain A: D.53, G.85, Q.87, D.89 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.53, A:G.85, A:Q.87, A:D.89, H2O.1, H2O.2 CA.6: 4 residues within 4Å: Chain A: S.17, D.19, D.94, E.96 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.19, A:D.94, A:E.96, H2O.5, H2O.5

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 4 residues within 4Å: Chain A: Y.67, H.78, A.79, F.80 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.79 pi-Cation interactions: A:Y.67, A:H.78, A:F.80 DMS.8: 1 residues within 4Å: Chain A: R.50 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.50 Water bridges: A:R.50

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

EDO.9: 4 residues within 4Å: Chain A: I.13, Q.14, Y.16, R.22 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.13, A:R.22 Water bridges: A:R.22 EDO.10: 5 residues within 4Å: Chain A: S.99, G.101, K.102, G.103, V.104 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.99, A:G.101, A:G.103 Water bridges: A:L.100 EDO.11: 3 residues within 4Å: Chain A: H.6, H.7, N.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.7, A:N.8 EDO.12: 3 residues within 4Å: Chain A: G.74, L.75 Ligands: N73.1 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 7 residues within 4Å: Chain A: D.1, K.3, W.4, H.5, H.6, P.82, G.83 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.3, A:H.5, A:H.6, A:H.6

2 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.14: 1 residues within 4Å: Chain A: R.50 No protein-ligand interaction detected (PLIP) PGO.15: 6 residues within 4Å: Chain A: P.128, E.129, A.130, R.137, T.139 Ligands: N73.1 No protein-ligand interaction detected (PLIP)

1 x BUD: (2S,3S)-butane-2,3-diol(Non-covalent)

BUD.16: 3 residues within 4Å: Chain A: E.18, L.20, P.21 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

2015-04-22

Peptides

Matrix metalloproteinase-9,Matrix metalloproteinase-9: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Matrix metalloproteinase-9,Matrix metalloproteinase-9

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