SMTL ID : 1you.3 (2 other biounits)

Crystal structure of the catalytic domain of MMP-13 complexed with a potent pyrimidinetrione inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.119, H.123, H.129 Ligands: PFD.6 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: 4 residues within 4Å: Chain B: H.119, H.123, H.129 Ligands: PFD.11 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 ZN.12: 4 residues within 4Å: Chain C: H.119, H.123, H.129 Ligands: PFD.17 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.119, C:H.123, C:H.129 ZN.13: 4 residues within 4Å: Chain C: H.69, D.71, H.84, H.97 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.69, C:D.71, C:H.84, C:H.97 ZN.18: 4 residues within 4Å: Chain D: H.119, H.123, H.129 Ligands: PFD.22 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.119, D:H.123, D:H.129 ZN.19: 4 residues within 4Å: Chain D: H.69, D.71, H.84, H.97 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.69, D:D.71, D:H.84, D:H.97

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 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.9: 7 residues within 4Å: Chain B: D.76, G.77, P.78, 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.14: 7 residues within 4Å: Chain C: D.76, G.77, P.78, S.79, L.81, D.99, E.102 6 PLIP interactions: 6 interactions with chain C Metal complexes: C:D.76, C:G.77, C:S.79, C:L.81, C:D.99, C:E.102 CA.20: 7 residues within 4Å: Chain D: D.76, G.77, P.78, S.79, L.81, D.99, E.102 6 PLIP interactions: 6 interactions with chain D Metal complexes: D:D.76, D:G.77, D:S.79, D:L.81, D:D.99, D:E.102

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: T.27, H.28 Chain D: T.27, H.28 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:H.28, A:H.28 Salt bridges: D:H.28, A:H.28 SO4.5: 3 residues within 4Å: Chain A: K.12, M.13, N.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.13, A:N.14, A:N.14 SO4.10: 3 residues within 4Å: Chain B: K.12, M.13, N.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.13, B:N.14, B:N.14 SO4.15: 4 residues within 4Å: Chain B: T.27, H.28 Chain C: T.27, H.28 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:H.28, C:H.28 Salt bridges: B:H.28, C:H.28 SO4.16: 3 residues within 4Å: Chain C: K.12, M.13, N.14 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:M.13, C:N.14, C:N.14 SO4.21: 3 residues within 4Å: Chain D: K.12, M.13, N.14 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:M.13, D:N.14, D:N.14

4 x PFD: 5-(2-ETHOXYETHYL)-5-[4-(4-FLUOROPHENOXY)PHENOXY]PYRIMIDINE-2,4,6(1H,3H,5H)-TRIONE(Non-covalent)

PFD.6: 16 residues within 4Å: Chain A: L.81, L.82, A.83, H.84, V.116, H.119, E.120, H.123, H.129, L.136, F.138, P.139, I.140, Y.141, T.142 Ligands: ZN.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.116, A:H.119, A:Y.141, A:Y.141 Hydrogen bonds: A:A.83, A:A.83 PFD.11: 18 residues within 4Å: Chain B: L.81, L.82, A.83, H.84, L.115, V.116, H.119, E.120, H.123, H.129, A.135, L.136, F.138, P.139, I.140, Y.141, T.142 Ligands: ZN.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.81, B:V.116, B:H.119, B:Y.141 Hydrogen bonds: B:L.82, B:A.83, B:A.83 pi-Cation interactions: B:H.119 PFD.17: 16 residues within 4Å: Chain C: L.81, L.82, A.83, H.84, V.116, H.119, E.120, H.123, H.129, L.136, F.138, P.139, I.140, Y.141, T.142 Ligands: ZN.12 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:V.116, C:H.119, C:Y.141, C:Y.141 Hydrogen bonds: C:L.82, C:A.83, C:A.83, C:H.123 PFD.22: 18 residues within 4Å: Chain D: L.81, L.82, A.83, H.84, L.115, V.116, H.119, E.120, H.123, H.129, A.135, L.136, F.138, P.139, I.140, Y.141, T.142 Ligands: ZN.18 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.81, D:V.116, D:H.119, D:Y.141 Hydrogen bonds: D:L.82, D:A.83, D:A.83 pi-Cation interactions: D:H.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blagg, J.A. et al., Potent pyrimidinetrione-based inhibitors of MMP-13 with enhanced selectivity over MMP-14. Bioorg.Med.Chem.Lett. (2005)

Release Date

2005-03-15

Peptides

Collagenase 3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Collagenase 3

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