SMTL ID : 7g5z.1

Crystal Structure of rat Autotaxin in complex with N-(5-chloro-2,3-dihydro-1H-inden-2-yl)-6-(5-methylpyrimidin-2-yl)-5,7-dihydropyrrolo[3,4-d]pyrimidin-2-amine, i.e. SMILES Clc1cc2c(cc1)C[C@@H](C2)Nc1ncc2CN(Cc2n1)c1ncc(cn1)C with IC50=0.0693825 microM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.44 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: 14 residues within 4Å: Chain A: L.193, E.196, S.197, H.198, G.228, H.406, N.409, N.410, P.495, N.496, N.497, D.716, L.718, H.804 No protein-ligand interaction detected (PLIP)

1 x Y9I: N-[(2S)-5-chloro-2,3-dihydro-1H-inden-2-yl]-6-(5-methylpyrimidin-2-yl)-6,7-dihydro-5H-pyrrolo[3,4-d]pyrimidin-2-amine(Non-covalent)

Y9I.2: 12 residues within 4Å: Chain A: I.140, S.142, T.182, F.183, L.186, L.189, L.216, F.246, F.247, W.248, A.277, Y.279 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.183, A:L.186, A:L.216, A:F.247, A:A.277 Hydrogen bonds: A:F.246, A:W.248 pi-Stacking: A:F.183, A:F.246, A:Y.279

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: F.681, V.684, P.769, R.771, D.773, N.774, L.791 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.771, A:R.771 EDO.4: 8 residues within 4Å: Chain A: E.123, I.124, C.167, G.168, Y.463, G.464, K.468, Y.469 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.124, A:I.124, A:G.464, A:R.508

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 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 CA.10: 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.16

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

ACT.6: 4 residues within 4Å: Chain A: V.420, D.421, R.422, V.453 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.453 Hydrogen bonds: A:R.422 Salt bridges: A:R.422 ACT.7: 7 residues within 4Å: Chain A: K.181, G.202, N.203, S.204, V.358, L.362, R.364 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.358, A:L.362 Hydrogen bonds: A:N.203, A:S.204 Salt bridges: A:R.364

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 3 residues within 4Å: Chain A: D.284, H.288, H.447 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.284, A:D.284, A:H.288, A:H.447, H2O.21

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

NA.9: 4 residues within 4Å: Chain A: N.774, D.775, S.777, S.780 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.774, A:S.780 Water bridges: A:S.780

1 x K: POTASSIUM ION(Non-covalent)

K.11: 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.13, H2O.22, H2O.22

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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