SMTL ID : 4qkz.1

X-ray structure of the catalytic domain of MMP-8 with the inhibitor ML115

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.58, G.90, I.91, G.92, D.94 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.58, A:G.90, A:G.92, A:D.94, H2O.1, H2O.1 CA.2: 6 residues within 4Å: Chain A: D.75, G.76, N.78, I.80, D.98, E.101 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.75, A:G.76, A:N.78, A:I.80, A:D.98, A:E.101

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.68, D.70, H.83, H.96 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.68, A:D.70, A:H.83, A:H.96 ZN.4: 4 residues within 4Å: Chain A: H.118, H.122, H.128 Ligands: QZK.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.118, A:H.122, A:H.128

1 x QZK: {[(biphenyl-4-ylsulfonyl)amino]methanediyl}bis(phosphonic acid)(Non-covalent)

QZK.5: 15 residues within 4Å: Chain A: I.80, L.81, A.82, H.83, L.114, H.118, E.119, H.122, H.128, L.135, Y.137, P.138, N.139, Y.140 Ligands: ZN.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:H.118, A:L.135, A:Y.140 Hydrogen bonds: A:A.82, A:A.82, A:E.119, A:H.128 pi-Stacking: A:H.118

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.6: 8 residues within 4Å: Chain A: A.33, D.36, N.105, N.111, F.113, T.145, S.146, Y.148 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.111, A:T.145, A:Y.148 Water bridges: A:N.105, A:N.105, A:N.105, A:F.113 Salt bridges: A:D.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laghezza, A. et al., Bone-Seeking Matrix Metalloproteinase Inhibitors for the Treatment of Skeletal Malignancy. Pharmaceuticals (2020)

Release Date

2015-06-17

Peptides

Neutrophil collagenase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Neutrophil collagenase

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