SMTL ID : 7g6b.1

Crystal Structure of rat Autotaxin in complex with 6-chloro-9-[2-(oxan-2-yloxy)ethyl]-3,4-dihydro-2H-pyrido[3,4-b]indol-1-one, i.e. SMILES c1(ccc2c(c1)C1=C(N2CCO[C@H]2OCCCC2)C(=O)NCC1)Cl with IC50=4.25663 microM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 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: 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.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

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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.203, A:S.204 Water bridges: A:K.181, A:K.181, A:R.364, A:R.364 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 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

1 x XK5: 6-chloro-9-(2-{[(2S)-oxan-2-yl]oxy}ethyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indol-1-one(Non-covalent)

XK5.5: 11 residues within 4Å: Chain A: I.140, S.142, F.183, L.186, Y.187, W.227, 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.186, A:L.186, A:F.247, A:F.247, A:F.247 Hydrogen bonds: A:S.142, A:W.248, A:W.248

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 9 residues within 4Å: Chain A: W.116, D.119, D.120, C.121, E.122, K.163, H.321, R.322, Y.463 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.116, A:E.122, A:Y.463 Salt bridges: A:K.163, A:R.322 SO4.7: 7 residues within 4Å: Chain A: T.182, N.203, L.216, D.284, H.288, H.447 Ligands: ZN.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.182, A:N.203 Salt bridges: A:K.181, A:H.288, A:H.447

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain A: D.284, H.288, H.447 Ligands: SO4.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.284, A:D.284, A:H.288, A:H.447

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

NA.9: 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.777, A:S.780 NA.11: 3 residues within 4Å: Chain A: Y.642, D.645, M.648 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.642, 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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