SMTL ID : 4bty.1

Crystal structure of human vascular adhesion protein-1 in complex with pyridazinone inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: F.104, Q.107, N.111, S.113, P.137 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 8 residues within 4Å: Chain A: Y.422, S.423, H.424, D.702 Chain B: R.180, V.183, N.206, S.208 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.424

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA-MAN-MAN.2: 7 residues within 4Å: Chain B: F.104, Q.107, N.111, S.113, D.128, V.131, P.137 No protein-ligand interaction detected (PLIP)

2 x CU: COPPER (II) ION(Non-covalent)

CU.4: 3 residues within 4Å: Chain A: H.494, H.496, H.658 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.494, A:H.496, A:H.658 CU.12: 3 residues within 4Å: Chain B: H.494, H.496, H.658 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.494, B:H.496, B:H.658

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 7 residues within 4Å: Chain A: K.80, D.503, L.504, D.505, N.511, D.647, L.648 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.503, A:L.504, A:D.505, A:D.647, A:L.648 CA.6: 6 residues within 4Å: Chain A: E.546, K.612, E.615, F.637, N.639, E.641 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.546, A:F.637, A:E.641 CA.13: 7 residues within 4Å: Chain B: K.80, D.503, L.504, D.505, N.511, D.647, L.648 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.503, B:L.504, B:D.505, B:D.647, B:L.648 CA.14: 6 residues within 4Å: Chain B: E.546, K.612, E.615, F.637, N.639, E.641 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.546, B:F.637, B:E.641

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.7: 5 residues within 4Å: Chain A: R.180, N.206, S.208 Chain B: Y.422, S.423 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain A: N.268 No protein-ligand interaction detected (PLIP) NAG.9: 1 residues within 4Å: Chain A: N.566 No protein-ligand interaction detected (PLIP) NAG.10: 1 residues within 4Å: Chain A: N.640 No protein-ligand interaction detected (PLIP) NAG.15: 2 residues within 4Å: Chain B: N.566, H.567 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.566, B:H.567 NAG.16: 1 residues within 4Å: Chain B: N.640 No protein-ligand interaction detected (PLIP)

2 x JWF: 5-[4-(4-methylpiperazin-1-yl)phenylamino]-2-(4-chlorophenyl)-6-(1H-1,2,4-triazol-5-yl)-3(2H)-pyridazinone(Non-covalent)

JWF.11: 11 residues within 4Å: Chain A: F.147, Y.150, L.151, D.154, T.184, F.201, F.363, Y.368, L.443, H.736 Chain B: Y.422 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.147, A:F.147, A:Y.150, A:L.151, A:F.363, A:Y.368, A:L.443, A:L.443 Hydrogen bonds: A:T.184, A:Y.368, B:Y.422 pi-Stacking: A:Y.150, A:Y.150 JWF.17: 12 residues within 4Å: Chain A: Y.422 Chain B: F.147, Y.150, L.151, D.154, T.184, T.186, F.363, Y.368, L.442, L.443, H.736 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.147, B:L.151, B:F.363, B:Y.368 Hydrogen bonds: B:Y.368, A:Y.422 pi-Stacking: B:Y.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bligt-Linden, E. et al., Novel Pyridazinone Inhibitors for Vascular Adhesion Protein- 1 (Vap-1): Old Target - New Inhibition Mode. J.Med.Chem. (2013)

Release Date

2013-12-18

Peptides

MEMBRANE PRIMARY AMINE OXIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

MEMBRANE PRIMARY AMINE OXIDASE

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