SMTL ID : 5i3m.2 (3 other biounits)

Crystal structure of the catalytic domain of MMP-12 in complex with a selective sugar-conjugated thiourea-linked carboxylate zinc-chelator water-soluble inhibitor (DC31).

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

monomer

Ligands

1 x 67F: (2S)-2-{[2-({[(2R,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]carbamothioyl}amino)ethyl](biphenyl-4-ylsulfonyl)amino}-3-methylbutanoic acid (non-preferred name)(Non-covalent)

67F.1: 16 residues within 4Å: Chain A: I.76, L.77, A.78, H.79, L.110, T.111, H.114, Q.115, H.118, H.124, V.131, F.133, P.134, T.135, Y.136 Ligands: ZN.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.76, A:H.79, A:H.114, A:Y.136 Hydrogen bonds: A:L.77, A:A.78, A:A.78, A:Q.115 Water bridges: A:H.118, A:H.124 Salt bridges: A:H.114, A:H.118, A:H.124 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: 67F.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.64, D.66, H.79, H.92 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.64, A:D.66, A:H.79, A:H.92

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: D.54, G.86, I.87, G.88, D.90 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.54, A:G.86, A:G.88, A:D.90, H2O.2, H2O.2 CA.5: 3 residues within 4Å: Chain A: D.20, E.95, E.97 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.20, A:E.95, A:E.95, H2O.3, H2O.3 CA.6: 6 residues within 4Å: Chain A: D.71, G.72, G.74, I.76, D.94, E.97 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.71, A:G.72, A:G.74, A:I.76, A:D.94, A:E.97

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

PGO.7: 6 residues within 4Å: Chain A: L.122, G.123, H.124, S.125, D.149, D.150 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.123

2 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.8: 4 residues within 4Å: Chain A: H.68, H.79, A.80, F.81 No protein-ligand interaction detected (PLIP) DIO.9: 5 residues within 4Å: Chain A: Y.28, A.29, T.101, F.109, I.141 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.107

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

Macrophage metalloelastase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Macrophage metalloelastase

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