SMTL ID : 5i43.1 (3 other biounits)

Crystal structure of the catalytic domain of MMP-12 in complex with a selective sugar-conjugated triazole-linked carboxylate chelator water-soluble inhibitor (DC32).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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: 67M.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.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.3: 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.4: 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.2, H2O.3 CA.5: 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 67M: (2R)-2-[({1-[3-({(2R,3R,4R,5S,6R)-3-(acetylamino)-4,5-bis(acetyloxy)-6-[(acetyloxy)methyl]tetrahydro-2H-pyran-2-yl}oxy)propyl]-1H-1,2,3-triazol-4-yl}methyl)(biphenyl-4-ylsulfonyl)amino]-3-methylbutanoic acid (non-preferred name)(Non-covalent)

67M.6: 18 residues within 4Å: Chain A: G.74, G.75, 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.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.76, A:H.79, A:Y.136 Hydrogen bonds: A:G.75, A:L.77, A:A.78, A:A.78, A:Q.115 Salt bridges: A:H.114, A:H.118, A:H.124 pi-Stacking: A:H.114

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

EDO.7: 1 residues within 4Å: Chain A: N.142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.142 EDO.8: 7 residues within 4Å: Chain A: L.122, G.123, S.125, M.132, D.149, D.150, G.153 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.149, A:D.150 EDO.9: 4 residues within 4Å: Chain A: V.4, W.5, R.6, K.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.4, A:R.6 Water bridges: A:R.6 EDO.10: 1 residues within 4Å: Chain A: N.49 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.49 Water bridges: A:K.47 EDO.11: 1 residues within 4Å: Chain A: K.73 No protein-ligand interaction detected (PLIP) EDO.12: 5 residues within 4Å: Chain A: F.34, Q.35, S.38, K.44, F.45 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.34, A:S.38, A:F.45 EDO.13: 3 residues within 4Å: Chain A: N.16, F.59, A.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.15, A:N.16 EDO.14: 4 residues within 4Å: Chain A: Y.17, T.18, P.19, R.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.23 Water bridges: A:Y.17 EDO.15: 4 residues within 4Å: Chain A: K.32, T.101, F.109, I.141 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.101 Water bridges: A:N.107 EDO.16: 4 residues within 4Å: Chain A: G.62, F.70, D.71, G.72 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.61, A:A.63

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
A

Macrophage metalloelastase

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