SMTL ID : 1utz.1

Crystal Structure of MMP-12 complexed to (2R)-3-({[4-[(pyridin-4-yl)phenyl]-thien-2-yl}carboxamido)(phenyl)propanoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

9 x PF3: (2R)-3-({[4-[(PYRIDIN-4-YL)PHENYL]-THIEN-2-YL}CARBOXAMIDO)(PHENYL)PROPANOIC ACID(Non-covalent)

PF3.1: 20 residues within 4Å: Chain A: G.74, I.75, L.76, A.77, L.109, H.113, E.114, A.129, V.130, F.132, P.133, T.134, Y.135, K.136, F.143 Chain B: S.124, S.125, P.133 Ligands: PF3.2, HAE.3 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.75, A:L.76, A:H.113, A:V.130, A:Y.135, B:P.133 Hydrogen bonds: A:P.133, A:P.133, A:Y.135 PF3.2: 14 residues within 4Å: Chain A: S.125, P.127, F.132, P.133, T.134 Chain B: D.70, K.72, G.73, G.74, F.132, P.133, T.134 Ligands: PF3.1, PF3.8 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.127, A:F.132, A:P.133, B:D.70, B:P.133 Hydrogen bonds: A:S.125 PF3.8: 20 residues within 4Å: Chain A: H.123, S.124 Chain B: G.74, I.75, L.76, A.77, L.109, T.110, H.113, E.114, A.129, V.130, F.132, P.133, T.134, Y.135, K.136, V.138 Ligands: PF3.2, HAE.9 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.76, B:H.113, B:Y.135, B:Y.135, A:H.123 Hydrogen bonds: B:L.76, B:A.77, B:P.133, B:P.133, B:Y.135 Water bridges: B:K.136 PF3.14: 20 residues within 4Å: Chain C: G.74, I.75, L.76, A.77, L.109, H.113, E.114, A.129, V.130, F.132, P.133, T.134, Y.135, K.136, F.143 Chain D: S.124, S.125, P.133 Ligands: PF3.15, HAE.16 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.75, C:L.76, C:H.113, C:Y.135, D:P.133 Hydrogen bonds: C:L.76, C:P.133, C:P.133, C:Y.135 PF3.15: 14 residues within 4Å: Chain C: S.125, P.127, F.132, P.133, T.134 Chain D: D.70, K.72, G.73, G.74, F.132, P.133, T.134 Ligands: PF3.14, PF3.21 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:P.127, C:F.132, C:P.133, D:D.70, D:P.133 Hydrogen bonds: C:S.125 PF3.21: 20 residues within 4Å: Chain C: H.123, S.124 Chain D: G.74, I.75, L.76, A.77, L.109, T.110, H.113, E.114, A.129, V.130, F.132, P.133, T.134, Y.135, K.136, V.138 Ligands: PF3.15, HAE.22 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.76, D:H.113, D:Y.135, D:Y.135, C:H.123 Hydrogen bonds: D:L.76, D:A.77, D:P.133, D:P.133, D:Y.135 Water bridges: D:K.136 PF3.27: 20 residues within 4Å: Chain E: G.74, I.75, L.76, A.77, L.109, H.113, E.114, A.129, V.130, F.132, P.133, T.134, Y.135, K.136, F.143 Chain F: S.124, S.125, P.133 Ligands: PF3.28, HAE.29 10 PLIP interactions: 9 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:I.75, E:L.76, E:H.113, E:V.130, E:Y.135, F:P.133 Hydrogen bonds: E:L.76, E:P.133, E:P.133, E:Y.135 PF3.28: 14 residues within 4Å: Chain E: S.125, P.127, F.132, P.133, T.134 Chain F: D.70, K.72, G.73, G.74, F.132, P.133, T.134 Ligands: PF3.27, PF3.34 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:P.127, E:F.132, E:P.133, F:D.70, F:P.133 Hydrogen bonds: E:S.125 PF3.34: 20 residues within 4Å: Chain E: H.123, S.124 Chain F: G.74, I.75, L.76, A.77, L.109, T.110, H.113, E.114, A.129, V.130, F.132, P.133, T.134, Y.135, K.136, V.138 Ligands: PF3.28, HAE.35 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:L.76, F:H.113, F:Y.135, F:Y.135, E:H.123 Hydrogen bonds: F:L.76, F:A.77, F:P.133, F:P.133, F:Y.135 Water bridges: F:K.136

6 x HAE: ACETOHYDROXAMIC ACID(Non-covalent)

HAE.3: 8 residues within 4Å: Chain A: A.77, H.78, H.113, E.114, H.117, H.123 Ligands: PF3.1, ZN.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.77 HAE.9: 8 residues within 4Å: Chain B: A.77, H.78, H.113, E.114, H.117, H.123 Ligands: PF3.8, ZN.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.77 HAE.16: 8 residues within 4Å: Chain C: A.77, H.78, H.113, E.114, H.117, H.123 Ligands: PF3.14, ZN.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.77 HAE.22: 8 residues within 4Å: Chain D: A.77, H.78, H.113, E.114, H.117, H.123 Ligands: PF3.21, ZN.23 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.77 HAE.29: 8 residues within 4Å: Chain E: A.77, H.78, H.113, E.114, H.117, H.123 Ligands: PF3.27, ZN.30 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:A.77 HAE.35: 8 residues within 4Å: Chain F: A.77, H.78, H.113, E.114, H.117, H.123 Ligands: PF3.34, ZN.36 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:A.77

12 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: H.113, H.117, H.123 Ligands: HAE.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.113, A:H.117, A:H.123, HAE.3 ZN.5: 4 residues within 4Å: Chain A: H.63, D.65, H.78, H.91 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.63, A:D.65, A:H.78, A:H.91 ZN.10: 4 residues within 4Å: Chain B: H.113, H.117, H.123 Ligands: HAE.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.113, B:H.117, B:H.123, HAE.9 ZN.11: 4 residues within 4Å: Chain B: H.63, D.65, H.78, H.91 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.63, B:D.65, B:H.78, B:H.91 ZN.17: 4 residues within 4Å: Chain C: H.113, H.117, H.123 Ligands: HAE.16 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.113, C:H.117, C:H.123, HAE.16 ZN.18: 4 residues within 4Å: Chain C: H.63, D.65, H.78, H.91 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.63, C:D.65, C:H.78, C:H.91 ZN.23: 4 residues within 4Å: Chain D: H.113, H.117, H.123 Ligands: HAE.22 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:H.113, D:H.117, D:H.123, HAE.22 ZN.24: 4 residues within 4Å: Chain D: H.63, D.65, H.78, H.91 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.63, D:D.65, D:H.78, D:H.91 ZN.30: 4 residues within 4Å: Chain E: H.113, H.117, H.123 Ligands: HAE.29 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:H.113, E:H.117, E:H.123, HAE.29 ZN.31: 4 residues within 4Å: Chain E: H.63, D.65, H.78, H.91 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.63, E:D.65, E:H.78, E:H.91 ZN.36: 4 residues within 4Å: Chain F: H.113, H.117, H.123 Ligands: HAE.35 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:H.113, F:H.117, F:H.123, HAE.35 ZN.37: 4 residues within 4Å: Chain F: H.63, D.65, H.78, H.91 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.63, F:D.65, F:H.78, F:H.91

12 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: D.70, G.71, G.73, I.75, D.93, E.96 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.70, A:G.71, A:G.73, A:I.75, A:D.93, A:E.96 CA.7: 3 residues within 4Å: Chain A: D.19, E.94, E.96 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.19, A:E.94, A:E.94, A:E.96 CA.12: 6 residues within 4Å: Chain B: D.70, G.71, G.73, I.75, D.93, E.96 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:D.70, B:G.71, B:G.73, B:I.75, B:D.93, B:E.96 CA.13: 3 residues within 4Å: Chain B: D.19, E.94, E.96 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.19, B:D.19, B:E.94, B:E.94, B:E.96 CA.19: 6 residues within 4Å: Chain C: D.70, G.71, G.73, I.75, D.93, E.96 6 PLIP interactions: 6 interactions with chain C Metal complexes: C:D.70, C:G.71, C:G.73, C:I.75, C:D.93, C:E.96 CA.20: 3 residues within 4Å: Chain C: D.19, E.94, E.96 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.19, C:E.94, C:E.94, C:E.96 CA.25: 6 residues within 4Å: Chain D: D.70, G.71, G.73, I.75, D.93, E.96 6 PLIP interactions: 6 interactions with chain D Metal complexes: D:D.70, D:G.71, D:G.73, D:I.75, D:D.93, D:E.96 CA.26: 3 residues within 4Å: Chain D: D.19, E.94, E.96 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.19, D:D.19, D:E.94, D:E.94, D:E.96 CA.32: 6 residues within 4Å: Chain E: D.70, G.71, G.73, I.75, D.93, E.96 6 PLIP interactions: 6 interactions with chain E Metal complexes: E:D.70, E:G.71, E:G.73, E:I.75, E:D.93, E:E.96 CA.33: 3 residues within 4Å: Chain E: D.19, E.94, E.96 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.19, E:E.94, E:E.94, E:E.96 CA.38: 6 residues within 4Å: Chain F: D.70, G.71, G.73, I.75, D.93, E.96 6 PLIP interactions: 6 interactions with chain F Metal complexes: F:D.70, F:G.71, F:G.73, F:I.75, F:D.93, F:E.96 CA.39: 3 residues within 4Å: Chain F: D.19, E.94, E.96 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.19, F:D.19, F:E.94, F:E.94, F:E.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morales, R. et al., Crystal Structures of Novel Non-Peptidic, Non-Zinc Chelating Inhibitors Bound to Mmp-12. J.Mol.Biol. (2004)

Release Date

2004-12-15

Peptides

MACROPHAGE METALLOELASTASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

MACROPHAGE METALLOELASTASE

Related Entries With Identical Sequence