SMTL ID : 7g4h.1

Crystal Structure of rat Autotaxin in complex with [2-methyl-4-(trifluoromethoxy)phenyl]methyl 2-(1,4,6,7-tetrahydrotriazolo[4,5-c]pyridine-5-carbonyl)-6,7-dihydro-4H-pyrazolo[1,5-a]pyrazine-5-carboxylate, i.e. SMILES N1(CCN2C(=CC(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1)C(=O)OCc1c(cc(cc1)OC(F)(F)F)C with IC50=0.268343 microM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

monomer

Ligands

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

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1: 12 residues within 4Å: Chain A: L.193, E.196, S.197, H.198, G.228, N.409, N.410, P.495, N.496, N.497, L.718, H.804 No protein-ligand interaction detected (PLIP)

1 x YNB: [2-methyl-4-(trifluoromethoxy)phenyl]methyl (8R)-2-(1,4,6,7-tetrahydro-5H-[1,2,3]triazolo[4,5-c]pyridine-5-carbonyl)-6,7-dihydropyrazolo[1,5-a]pyrazine-5(4H)-carboxylate(Non-covalent)

YNB.2: 16 residues within 4Å: Chain A: I.140, D.144, F.183, L.186, L.189, A.190, F.246, F.247, W.248, V.250, Y.279, E.281, D.284, F.285, M.485 Ligands: ACT.9 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.186, A:F.246, A:F.247, A:V.250, A:E.281 Hydrogen bonds: A:W.248, A:D.284

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: D.284, H.288, H.447 Ligands: ACT.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.284, A:D.284, A:H.288, A:H.447

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

NA.4: 4 residues within 4Å: Chain A: N.774, D.775, S.777, S.780 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.774

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: D.712, N.714, D.716, L.718, D.720 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.712, A:D.716, A:L.718, A:D.720, H2O.12 CA.8: 4 residues within 4Å: Chain A: D.144, T.182, D.331, H.332 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.144, A:D.144, A:T.182, A:D.331, A:H.332

1 x K: POTASSIUM ION(Non-covalent)

K.6: 4 residues within 4Å: Chain A: Y.642, D.645, M.648 Ligands: ACT.11 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:Y.642, A:D.645, A:M.648, H2O.11, ACT.11

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 4 residues within 4Å: Chain A: K.181, G.202, N.203, R.364 Ligand excluded by PLIP

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 7 residues within 4Å: Chain A: D.144, T.182, D.284, H.288, H.447 Ligands: YNB.2, ZN.3 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.288, A:H.447 ACT.10: 6 residues within 4Å: Chain A: V.420, D.421, R.422, D.450, K.452, V.453 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:D.450, A:V.453 Hydrogen bonds: A:R.422 Water bridges: A:R.422, A:K.452 Salt bridges: A:R.422, A:K.452 ACT.11: 4 residues within 4Å: Chain A: Y.642, M.648, S.649 Ligands: K.6 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.682

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hunziker, D. et al., Crystal Structure of a rat Autotaxin complex. To be published

Release Date

2024-12-18

Peptides

Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

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