SMTL ID : 7g6w.1

Crystal Structure of rat Autotaxin in complex with N-[(3,4-dichlorophenyl)methyl]-2-[4-oxo-6-[4-(oxolan-3-ylmethyl)piperazin-1-yl]quinazolin-3-yl]acetamide, i.e. SMILES O=C1N(CC(=O)NCc2cc(Cl)c(Cl)cc2)C=Nc2c1cc(N1CCN(C[C@H]3CCOC3)CC1)cc2 with IC50=0.0358891 microM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 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 XJQ: N-[(3,4-dichlorophenyl)methyl]-2-[4-oxo-6-(4-{[(3S)-oxolan-3-yl]methyl}piperazin-1-yl)quinazolin-3(4H)-yl]acetamide(Non-covalent)

XJQ.2: 15 residues within 4Å: Chain A: L.51, S.54, Y.55, F.183, L.186, Y.187, K.221, F.222, H.224, W.227, W.233, F.246, F.247, W.248, Y.279 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.55, A:L.186, A:F.222, A:F.222, A:F.247, A:F.247 Hydrogen bonds: A:S.54, A:W.248 pi-Cation interactions: A:K.221 Halogen bonds: A:F.183

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

MES.3: 8 residues within 4Å: Chain A: K.181, G.202, N.203, S.204, V.358, P.359, L.362, R.364 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.203, A:S.204, A:S.204 Water bridges: A:K.181, A:K.181 Salt bridges: A:K.181, A:R.364

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

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: D.144, T.182, D.331, H.332 4 PLIP interactions: 4 interactions with chain A Metal complexes: 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.18

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

CL.6: 2 residues within 4Å: Chain A: S.56, C.58 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 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.19

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

NA.8: 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:S.777, A:S.780 Water bridges: A:S.780 NA.10: 3 residues within 4Å: Chain A: Y.642, D.645, M.648 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.645, A:M.648

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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