SMTL ID : 5bpa.1

X-RAY Co-structure of MMP-13 with 4-[({5-[2-(ethoxycarbonyl)-1H-indol-5-yl]-1-methyl-1H-pyrazol-3-yl}formamido)methyl]benzoate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.119, H.123, H.129 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.119, A:H.123, A:H.129 ZN.2: 4 residues within 4Å: Chain A: H.69, D.71, H.84, H.97 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.69, A:D.71, A:H.84, A:H.97 ZN.7: 3 residues within 4Å: Chain B: H.119, H.123, H.129 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.119, B:H.123, B:H.129 ZN.8: 4 residues within 4Å: Chain B: H.69, D.71, H.84, H.97 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.69, B:D.71, B:H.84, B:H.97

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: T.23, D.25, D.100, E.102 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.25, A:D.100, A:D.100, A:E.102 CA.4: 6 residues within 4Å: Chain A: D.76, G.77, S.79, L.81, D.99, E.102 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.76, A:G.77, A:S.79, A:L.81, A:D.99, A:E.102 CA.5: 6 residues within 4Å: Chain A: A.58, D.59, N.91, Y.92, G.93, D.95 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.59, A:N.91, A:G.93, A:D.95, H2O.1 CA.9: 4 residues within 4Å: Chain B: T.23, D.25, D.100, E.102 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.25, B:D.100, B:D.100, B:E.102 CA.10: 6 residues within 4Å: Chain B: D.76, G.77, S.79, L.81, D.99, E.102 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:D.76, B:G.77, B:S.79, B:L.81, B:D.99, B:E.102 CA.11: 6 residues within 4Å: Chain B: A.58, D.59, N.91, Y.92, G.93, D.95 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.59, B:N.91, B:G.93, B:D.95

2 x 4UF: 4-{[({5-[2-(ethoxycarbonyl)-1H-indol-5-yl]-1-methyl-1H-pyrazol-3-yl}carbonyl)amino]methyl}benzoic acid(Non-covalent)

4UF.6: 20 residues within 4Å: Chain A: K.37, L.82, N.112, F.114, L.115, H.119, E.120, A.135, L.136, F.138, P.139, I.140, Y.141, T.142, Y.143, T.144, K.146, H.148, F.149, P.152 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.82, A:F.114, A:L.136, A:F.149 Hydrogen bonds: A:N.112, A:N.112, A:F.138, A:I.140, A:T.144 Water bridges: A:K.37 Salt bridges: A:K.37, A:H.119 4UF.12: 22 residues within 4Å: Chain B: K.37, S.106, N.112, F.114, L.115, V.116, H.119, E.120, A.135, L.136, F.138, P.139, I.140, Y.141, T.142, Y.143, T.144, K.146, S.147, H.148, F.149, P.152 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.114, B:L.115, B:V.116, B:L.136 Hydrogen bonds: B:N.112, B:N.112, B:F.138, B:I.140, B:T.144 Water bridges: B:K.37, B:T.144, B:G.145, B:H.148 Salt bridges: B:K.37, B:H.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Taylor, S.J. et al., Fragment-based discovery of indole inhibitors of matrix metalloproteinase-13. J. Med. Chem. (2011)

Release Date

2015-06-17

Peptides

Collagenase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Collagenase 3

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