SMTL ID : 5my8.1

Crystal structure of SRPK1 in complex with SPHINX31

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.1: 4 residues within 4Å: Chain A: R.243, R.246, R.289 Ligands: GOL.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.289 Water bridges: A:R.243 Salt bridges: A:R.243, A:R.246, A:R.246, A:R.289

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: D.158, N.228, D.239, Q.241, T.242, R.246 Ligands: CIT.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.158, A:D.239 Water bridges: A:K.160, A:N.228, A:N.228, A:N.228, A:N.228, A:D.239, A:Q.241

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 7 residues within 4Å: Chain A: F.270, Y.277, L.278, W.334, K.343, Y.344 Ligands: EDO.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.343, A:Y.344

20 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 2 residues within 4Å: Chain A: G.32, W.33 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: L.376, R.377, H.378, P.379, L.381, N.382 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: T.150, K.151, R.153 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: W.231, H.233 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: D.83, N.85, D.146, Y.147, T.150, K.151 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: N.257, P.259, E.367 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: V.310, A.311, G.312, K.313 Ligand excluded by PLIP EDO.11: 1 residues within 4Å: Chain A: Y.314 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: L.131, W.346, E.350 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: N.85, Q.139, Q.143, L.376 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: W.334, V.339, K.343 Ligands: DMS.3 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain A: K.343, E.345 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: L.31, H.115, Y.172, L.176 Ligands: RXZ.24 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain A: W.43, F.50 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain A: R.153, H.233 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: P.360, K.368, R.369, A.370, E.374 Ligands: EDO.22 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: H.282, Y.287, D.292, I.328 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: E.285, E.286, T.288 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: D.356, P.360, H.378 Ligands: EDO.19 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: S.75, S.79, C.152, R.153, W.231 Ligand excluded by PLIP

1 x RXZ: SPHINX31(Non-covalent)

RXZ.24: 21 residues within 4Å: Chain A: L.31, W.33, G.34, S.37, V.39, A.52, K.54, F.110, E.111, V.112, L.113, G.114, H.115, L.165, V.168, Y.172, I.173, L.176, A.224, D.225 Ligands: EDO.16 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.31, A:V.39, A:A.52, A:F.110, A:F.110, A:L.113 Hydrogen bonds: A:L.113 pi-Stacking: A:H.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Batson, J. et al., Development of Potent, Selective SRPK1 Inhibitors as Potential Topical Therapeutics for Neovascular Eye Disease. ACS Chem. Biol. (2017)

Release Date

2017-05-10

Peptides

SRSF protein kinase 1,SRSF protein kinase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

SRSF protein kinase 1,SRSF protein kinase 1

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