SMTL ID : 5i12.1

Crystal structure of the catalytic domain of MMP-9 in complex with a selective sugar-conjugated arylsulfonamide carboxylate water-soluble inhibitor (DC27).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.114, H.118, H.124 Ligands: H27.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.114, A:H.118, A:H.124 ZN.2: 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.3: 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.4: 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.1 CA.5: 4 residues within 4Å: Chain A: S.17, D.19, D.94, E.96 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.19, A:D.94, A:D.94, A:E.96, H2O.2

1 x H27: (2R)-2-[{(E)-2-[({(2R,3R,4R,5S,6R)-3-(acetylamino)-4,5-bis(acetyloxy)-6-[(acetyloxy)methyl]tetrahydro-2H-pyran-2-yl}carbamothioyl)amino]ethenyl}(biphenyl-4-ylsulfonyl)amino]-3-methylbutanoic acid(Non-covalent)

H27.6: 17 residues within 4Å: Chain A: 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.1, GOL.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.75, A:H.114, A:Y.136 Hydrogen bonds: A:A.77 Salt bridges: A:H.114, A:H.118, A:H.124 pi-Stacking: A:H.114

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

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

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

DMS.8: 4 residues within 4Å: Chain A: Y.67, H.78, A.79, F.80 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.79 pi-Cation interactions: A:Y.67, A:F.80

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: P.128, E.129, A.130, R.137, T.139 Ligands: H27.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.128, A:R.137 Water bridges: A:T.139, A:T.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nuti, E. et al., Sugar-Based Arylsulfonamide Carboxylates as Selective and Water-Soluble Matrix Metalloproteinase-12 Inhibitors. Chemmedchem (2016)

Release Date

2016-07-06

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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