SMTL ID : 7ocb.1

Crystal structure of Spindlin1 in complex with the inhibitor XY49-92B

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

monomer

Ligands

1 x V88: 7-[3-(1,3-dihydroisoindol-2-yl)propoxy]-2N-[2-(dimethylamino)ethyl]-6-methoxy-4N-(1-propan-2-ylpiperidin-4-yl)quinazoline-2,4-diamine(Non-covalent)

V88.1: 13 residues within 4Å: Chain A: D.48, H.92, M.93, F.94, W.104, Y.123, Y.130, Y.132, D.136, D.137, E.140, D.142 Ligands: CL.5 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.94, A:F.94, A:F.94, A:W.104, A:W.104, A:Y.123 Hydrogen bonds: A:Y.132, A:D.137 Water bridges: A:H.92, A:D.136, A:D.142, A:D.142 Salt bridges: A:D.136, A:D.137 pi-Cation interactions: A:W.104

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 3 residues within 4Å: Chain A: P.34, V.35, P.37 No protein-ligand interaction detected (PLIP)

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 12 residues within 4Å: Chain A: R.105, G.106, M.107, L.109, T.122, Y.123, E.124, P.127, V.195, V.208, Y.209, D.210 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.124, A:V.195, A:V.208, A:D.210 Water bridges: A:D.210 MPD.4: 9 residues within 4Å: Chain A: H.13, W.15, W.25, Y.44, F.47, Y.51, L.53, F.204 Ligands: GLY.6 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.15, A:W.25, A:W.25, A:F.204, A:F.204 Water bridges: A:Y.51 Hydrogen bonds: G.6

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

CL.5: 3 residues within 4Å: Chain A: F.94, E.95 Ligands: V88.1 Ligand excluded by PLIP

1 x GLY: GLYCINE(Non-covalent)

GLY.6: 4 residues within 4Å: Chain A: E.17, W.25, F.204 Ligands: MPD.4 No protein-ligand interaction detected (PLIP)

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

NA.7: 2 residues within 4Å: Chain A: K.101, E.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.101, A:E.140 NA.8: 4 residues within 4Å: Chain A: R.60, D.202, D.203, F.204 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.60, A:R.60, A:F.204 Water bridges: A:D.202, A:D.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, C. et al., Crystal structure of Spindlin1 in complex with the inhibitor XY49-92B. To Be Published

Release Date

2022-05-04

Peptides

Spindlin-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Spindlin-1

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