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SMTL ID : 7g60.1

Crystal Structure of rat Autotaxin in complex with (2S)-6-chloro-2-[(6-methylsulfonyl-5,7-dihydropyrrolo[3,4-d]pyrimidin-2-yl)amino]-2,3-dihydro-1H-indene-4-carbonitrile, i.e. SMILES N(c1nc2c(cn1)CN(S(=O)(=O)C)C2)[C@H]1Cc2c(C1)c(cc(c2)Cl)C#N with IC50=0.00218558 microM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- MAN- 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)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-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

2 PLIP interactions:

2 interactions with chain A

Water bridges: A:N.409, A:D.716

1 x YFI: (2R)-6-chloro-2-{[6-(methanesulfonyl)-6,7-dihydro-5H-pyrrolo[3,4-d]pyrimidin-2-yl]amino}-2,3-dihydro-1H-indene-4-carbonitrile(Non-covalent)

YFI.2:

14 residues within 4Å:

Chain A: I.140, S.142, T.182, F.183, L.186, Y.187, L.189, A.190, L.216, W.233, F.246, F.247, W.248, Y.279

8 PLIP interactions:

8 interactions with chain A

Hydrophobic interactions: A:L.186, A:A.190, A:F.247, A:Y.279
Hydrogen bonds: A:F.246, A:W.248
pi-Stacking: A:F.246, A:Y.279

2 x CA: CALCIUM ION(Non-covalent)

CA.3:	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.24

1 x K: POTASSIUM ION(Non-covalent)

K.4:	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.18, H₂O.27, H₂O.27

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

ACT.5:	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
ACT.6:	7 residues within 4Å: Chain A: K.181, G.202, N.203, S.204, V.358, L.362, R.364 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.358, A:L.362 Hydrogen bonds: A:N.203, A:S.204 Water bridges: A:K.181, A:T.361 Salt bridges: A:K.181, A:R.364
ACT.7:	7 residues within 4Å: Chain A: T.182, N.203, L.216, D.284, H.288, H.447 Ligands: ZN.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.216 Hydrogen bonds: A:N.203 Salt bridges: 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: ACT.7

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.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.780, 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

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

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