SMTL ID : 2yig.1

MMP13 in complex with a novel selective non zinc binding inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x 5EL: 4-(4-{[(3S)-3-HYDROXY-1-AZABICYCLO[2.2.2]OCT-3-YL]ETHYNYL}PHENOXY)-N-(PYRIDIN-4-YLMETHYL)BENZAMIDE(Non-covalent)

5EL.1: 16 residues within 4Å: Chain A: G.80, L.81, L.82, L.115, V.116, H.119, E.120, G.134, L.136, F.138, P.139, I.140, Y.141, T.142, T.144, F.149 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.81, A:L.82, A:V.116, A:Y.141 Hydrogen bonds: A:L.82, A:P.139, A:T.142, A:T.142, A:T.144 5EL.8: 17 residues within 4Å: Chain B: G.80, L.81, L.82, L.115, V.116, H.119, E.120, G.134, L.136, F.138, P.139, I.140, Y.141, T.142, T.144, F.149, P.152 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.81, B:L.81, B:L.115, B:H.119, B:Y.141, B:Y.141, B:F.149, B:P.152 Hydrogen bonds: B:A.83, B:P.139, B:T.142 Water bridges: B:T.142

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: H.119, H.123, H.129 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.119, A:H.123, A:H.129, H2O.4 ZN.4: 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.9: 3 residues within 4Å: Chain B: H.119, H.123, H.129 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.119, B:H.123, B:H.129, H2O.10 ZN.10: 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

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.59, N.91, Y.92, G.93, D.95 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.59, A:N.91, A:G.93, A:D.95, H2O.2, H2O.3 CA.5: 7 residues within 4Å: Chain A: D.76, G.77, P.78, 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.11: 5 residues within 4Å: Chain B: D.59, N.91, Y.92, G.93, D.95 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.59, B:N.91, B:G.93, B:D.95, H2O.7, H2O.7 CA.12: 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

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

NA.6: 4 residues within 4Å: Chain A: T.23, D.25, D.100, E.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.25 NA.7: 1 residues within 4Å: Chain A: A.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.85 Water bridges: A:A.85 NA.13: 4 residues within 4Å: Chain B: T.23, D.25, D.100, E.102 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Savi, C.D. et al., Selective Non Zinc Binding Inhibitors of Mmp13. Bioorg.Med.Chem.Lett. (2011)

Release Date

2011-06-29

Peptides

COLLAGENASE 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

COLLAGENASE 3

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