SMTL ID : 4btw.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA: 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.1: 6 residues within 4Å: Chain A: F.104, Q.107, N.111, S.113, V.131, P.137 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.104

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.2: 7 residues within 4Å: Chain A: R.180, N.206, S.208 Chain B: Y.422, S.423, H.424, D.702 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.424, B:D.702, B:D.702 NAG-NAG.4: 3 residues within 4Å: Chain A: D.702 Chain B: N.206, S.208 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.702

1 x NAG- NAG- BMA- MAN- BMA: alpha-D-mannopyranose-(1-3)-[beta-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-BMA.3: 5 residues within 4Å: Chain B: F.104, Q.107, N.111, S.113, P.137 No protein-ligand interaction detected (PLIP)

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

CU.5: 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.11: 3 residues within 4Å: Chain B: H.494, H.496, H.658 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.494, B:H.496, B:H.658, H2O.4

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: 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.7: 6 residues within 4Å: Chain A: E.546, K.612, E.615, F.637, N.639, E.641 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.546, A:E.546, A:F.637, A:E.641 CA.12: 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.13: 6 residues within 4Å: Chain B: E.546, K.612, E.615, F.637, N.639, E.641 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.546, B:E.546, B:E.615, B:F.637, B:E.641

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

NAG.8: 2 residues within 4Å: Chain A: N.566, H.567 No protein-ligand interaction detected (PLIP) NAG.9: 1 residues within 4Å: Chain A: N.640 No protein-ligand interaction detected (PLIP) NAG.14: 1 residues within 4Å: Chain B: N.268 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.268 NAG.15: 2 residues within 4Å: Chain B: N.566, H.567 No protein-ligand interaction detected (PLIP) NAG.16: 1 residues within 4Å: Chain B: N.592 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.592 NAG.17: 1 residues within 4Å: Chain B: N.640 No protein-ligand interaction detected (PLIP)

2 x JW7: 5-(cyclohexylamino)-2-phenyl-6-(1H-1,2,4-triazol-5-yl)-3(2H)-pyridazinone(Non-covalent)

JW7.10: 12 residues within 4Å: Chain A: F.147, Y.150, L.151, D.154, T.184, T.186, F.201, F.363, Y.368, L.443 Chain B: L.421, Y.422 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.150, A:L.151, A:L.151, A:T.186, A:F.363, A:Y.368, A:L.443, B:L.421 Hydrogen bonds: A:T.184, A:Y.368 pi-Stacking: B:Y.422 JW7.18: 10 residues within 4Å: Chain A: Y.422 Chain B: F.147, Y.150, D.154, T.184, T.186, F.201, F.363, Y.368, L.443 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.363, B:Y.368, B:Y.368, B:L.443, B:L.443 Hydrogen bonds: B:T.186, B:Y.368, A:Y.422

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

Related Entries With Identical Sequence