SMTL ID : 4jpa.1

Mmp13 in complex with a piperazine hydantoin ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.121, H.125, H.131 Ligands: AZ6.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.121, A:H.125, A:H.131 ZN.3: 4 residues within 4Å: Chain A: H.71, D.73, H.86, H.99 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.71, A:D.73, A:H.86, A:H.99 ZN.7: 4 residues within 4Å: Chain B: H.121, H.125, H.131 Ligands: AZ6.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.121, B:H.125, B:H.131 ZN.8: 4 residues within 4Å: Chain B: H.71, D.73, H.86, H.99 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.71, B:D.73, B:H.86, B:H.99

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.61, N.93, G.95, D.97 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.61, A:N.93, A:G.95, A:D.97, H2O.1, H2O.8 CA.4: 7 residues within 4Å: Chain A: D.78, G.79, P.80, S.81, L.83, D.101, E.104 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.78, A:G.79, A:S.81, A:L.83, A:D.101, A:E.104 CA.9: 6 residues within 4Å: Chain B: A.60, D.61, N.93, Y.94, G.95, D.97 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.61, B:N.93, B:G.95, B:D.97, H2O.9, H2O.9 CA.10: 6 residues within 4Å: Chain B: D.78, G.79, S.81, L.83, D.101, E.104 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:D.78, B:G.79, B:S.81, B:L.83, B:D.101, B:E.104

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 4 residues within 4Å: Chain A: T.25, D.27, D.102, E.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.27 NA.11: 4 residues within 4Å: Chain B: T.25, D.27, D.102, E.104 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.102

2 x AZ6: 3-[({2-[4-({[(4S)-4-methyl-2,5-dioxoimidazolidin-4-yl]methyl}sulfonyl)piperazin-1-yl]pyrimidin-5-yl}oxy)methyl]benzonitrile(Non-covalent)

AZ6.6: 21 residues within 4Å: Chain A: G.82, L.83, L.84, A.85, H.86, L.117, H.121, E.122, H.125, H.131, G.136, A.137, L.138, F.140, P.141, I.142, Y.143, T.144, Y.145, F.151 Ligands: ZN.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.151 Hydrogen bonds: A:L.84, A:A.85, A:A.85 Water bridges: A:A.87 Salt bridges: A:E.122 pi-Stacking: A:H.121 AZ6.12: 22 residues within 4Å: Chain B: G.82, L.83, L.84, A.85, H.86, L.117, H.121, E.122, H.125, H.131, G.136, A.137, L.138, F.140, P.141, I.142, Y.143, T.144, Y.145, T.146, F.151 Ligands: ZN.7 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.151 Hydrogen bonds: B:A.85, B:A.85, B:T.146 Water bridges: B:A.87, B:T.146 pi-Stacking: B:H.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

De Savi, C. et al., Hydantoin based inhibitors of MMP13--discovery of AZD6605. Bioorg.Med.Chem.Lett. (2013)

Release Date

2014-03-05

Peptides

Collagenase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Collagenase 3

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