SMTL ID : 7g2w.1

Crystal Structure of rat Autotaxin in complex with 4-[3-[(2-tert-butyl-4-chloro-5-methylphenyl)methoxy]-4,5,7,8-tetrahydro-1H-pyrazolo[3,4-d]azepine-6-carbonyl]benzenesulfonamide, i.e. SMILES c1(ccc(cc1)C(=O)N1CCC2=C(CC1)NN=C2OCc1c(cc(c(c1)C)Cl)C(C)(C)C)S(=O)(=O)N with IC50=0.0150328 microM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 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: 13 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, D.716, L.718, H.804 No protein-ligand interaction detected (PLIP)

2 x XJC: 4-{3-[(2-tert-butyl-4-chloro-5-methylphenyl)methoxy]-4,5,7,8-tetrahydropyrazolo[3,4-d]azepine-6(1H)-carbonyl}benzene-1-sulfonamide(Non-covalent)

XJC.2: 25 residues within 4Å: Chain A: I.140, S.142, D.144, K.181, T.182, F.183, L.186, Y.187, L.189, A.190, N.203, L.216, W.233, F.246, F.247, W.248, A.277, Y.279, D.284, H.288, H.332, H.447 Ligands: XJC.3, CA.5, ZN.10 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.140, A:L.186, A:L.186, A:Y.187, A:L.216, A:W.233, A:F.247, A:A.277, A:Y.279, A:Y.279 Hydrogen bonds: A:T.182, A:N.203, A:W.248, A:W.248 Water bridges: A:D.284 pi-Stacking: A:Y.279 XJC.3: 16 residues within 4Å: Chain A: L.38, L.51, Y.55, F.183, Y.187, K.221, F.222, H.224, W.227, W.233, A.243, G.244, T.245, F.246, F.247 Ligands: XJC.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.51, A:F.183, A:K.221, A:F.222, A:W.227, A:W.227, A:W.233, A:F.247 Hydrogen bonds: A:L.38, A:H.224, A:T.245, A:F.246, A:F.247 Water bridges: A:T.237, A:T.237, A:A.243, A:A.243 pi-Stacking: A:W.227, A:W.227

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 1 residues within 4Å: Chain A: D.45 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.45, A:D.45, H2O.21, H2O.23, H2O.30 CA.5: 5 residues within 4Å: Chain A: D.144, T.182, D.331, H.332 Ligands: XJC.2 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 CA.12: 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.20

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

ACT.6: 5 residues within 4Å: Chain A: V.420, D.421, R.422, D.450, V.453 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.450, A:V.453 Hydrogen bonds: A:R.422 Salt bridges: A:R.422 ACT.7: 4 residues within 4Å: Chain A: Y.642, M.648, S.649 Ligands: K.9 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.650, A:K.682 Salt bridges: A:K.682

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

CL.8: 4 residues within 4Å: Chain A: G.202, N.203, S.204, R.364 Ligand excluded by PLIP

1 x K: POTASSIUM ION(Non-covalent)

K.9: 4 residues within 4Å: Chain A: Y.642, D.645, M.648 Ligands: ACT.7 6 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:Y.642, A:D.645, A:M.648, ACT.7, H2O.21, H2O.24

1 x ZN: ZINC ION(Non-covalent)

ZN.10: 4 residues within 4Å: Chain A: D.284, H.288, H.447 Ligands: XJC.2 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.11: 4 residues within 4Å: Chain A: N.774, D.775, S.777, S.780 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.780, A:S.780

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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