SMTL ID : 7g5p.1

Crystal Structure of rat Autotaxin in complex with N-[(1R,3S)-3-[(2S)-2-benzyl-4-[2-(methylamino)-2-oxoethyl]-3-oxopiperazine-1-carbonyl]cyclopentyl]-4-chloro-3-(trifluoromethyl)benzamide, i.e. SMILES C1[C@@H](CC[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1Cc1ccccc1)CC(=O)NC)NC(=O)c1ccc(c(c1)C(F)(F)F)Cl with IC50=0.17269 microM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 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)

1 x Y8Z: N-[(1R,3R)-3-{(2S)-2-benzyl-4-[2-(methylamino)-2-oxoethyl]-3-oxopiperazine-1-carbonyl}cyclopentyl]-4-chloro-3-(trifluoromethyl)benzamide(Non-covalent)

Y8Z.2: 16 residues within 4Å: Chain A: I.140, S.142, F.183, L.186, Y.187, L.189, A.190, K.221, F.222, W.227, W.233, F.246, F.247, V.250, A.277, Y.279 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.183, A:F.183, A:L.186, A:L.186, A:K.221, A:F.222, A:F.222, A:W.227, A:W.227, A:W.227, A:F.247 Water bridges: A:V.250 pi-Stacking: A:F.247

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: D.284, H.288, H.447 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.284, A:H.288, A:H.447, H2O.1, H2O.21

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

NA.4: 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 NA.6: 3 residues within 4Å: Chain A: Y.642, D.645, M.648 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.648

1 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.19

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

ACT.7: 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

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.8: 8 residues within 4Å: Chain A: K.181, G.202, N.203, S.204, V.358, P.359, L.362, R.364 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.203, A:S.204 Water bridges: A:K.181, A:K.181 Salt bridges: A:K.181, A:R.364

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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