SMTL ID : 7g2q.1

Crystal Structure of rat Autotaxin in complex with 1-[2-[2-cyclopropyl-6-(oxan-4-ylmethoxy)pyridine-4-carbonyl]-1,3,4,6-tetrahydropyrrolo[3,4-c]pyrrole-5-carbonyl]piperidine-4-sulfonamide, i.e. SMILES N1(C(=O)N2CC3=C(CN(C3)C(=O)c3cc(nc(c3)C3CC3)OCC3CCOCC3)C2)CC[C@@H](CC1)S(=O)(=O)N with IC50=0.00248328 microM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 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 CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.144, T.182, D.331, H.332 Ligands: XF3.3 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.9: 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.15

1 x XF3: 1-[5-{2-cyclopropyl-6-[(oxan-4-yl)methoxy]pyridine-4-carbonyl}-3,4,5,6-tetrahydropyrrolo[3,4-c]pyrrole-2(1H)-carbonyl]piperidine-4-sulfonamide(Non-covalent)

XF3.3: 20 residues within 4Å: Chain A: I.140, S.142, D.144, T.182, F.183, L.186, Y.187, L.189, A.190, N.203, L.216, W.227, F.247, W.248, Y.279, D.284, H.288, H.447 Ligands: CA.2, ZN.7 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:T.182, A:F.183, A:L.186, A:L.186, A:Y.187, A:Y.187, A:A.190, A:W.227, A:F.247 Hydrogen bonds: A:T.182, A:N.203, A:W.248 Water bridges: A:S.142 pi-Stacking: A:F.247, A:Y.279

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

ACT.4: 5 residues within 4Å: Chain A: V.420, D.421, R.422, D.450, V.453 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.450 Hydrogen bonds: A:R.422 Salt bridges: A:R.422

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

CL.5: 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.6: 3 residues within 4Å: Chain A: Y.642, D.645, M.648 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:Y.642, A:D.645, A:M.648, H2O.12, H2O.15, H2O.16

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain A: D.284, H.288, H.447 Ligands: XF3.3 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.8: 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:N.774 Water bridges: 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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