SMTL ID : 5mxx.1

Crystal structure of human SR protein kinase 1 (SRPK1) in complex with compound 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x W4A: 5-methyl-~{N}-[2-(4-methylpiperazin-1-yl)-5-(trifluoromethyl)phenyl]furan-2-carboxamide(Non-covalent)

W4A.1: 14 residues within 4Å: Chain A: L.47, G.48, A.68, F.126, E.127, V.128, L.129, G.130, H.131, L.181, V.184, Y.188, L.192 Ligands: EDO.11 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.47, A:L.47, A:A.68, A:F.126, A:L.181 Hydrogen bonds: A:L.129, A:G.130 pi-Stacking: A:H.131

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

EDO.2: 2 residues within 4Å: Chain A: K.359, Y.360 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.359 EDO.3: 6 residues within 4Å: Chain A: D.99, N.101, D.162, Y.163, T.166, K.167 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.101, A:D.162, A:K.167 Water bridges: A:K.167 EDO.4: 2 residues within 4Å: Chain A: H.165, T.166 6 PLIP interactions: 6 interactions with chain A Water bridges: A:T.166, A:T.166, A:T.274, A:T.274, A:T.274, A:A.388 EDO.5: 6 residues within 4Å: Chain A: L.83, I.86, D.111, F.112, K.113, I.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.111 EDO.6: 1 residues within 4Å: Chain A: N.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.244 Water bridges: A:N.244 EDO.7: 4 residues within 4Å: Chain A: L.147, W.362, E.366 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.147, A:E.361 EDO.8: 5 residues within 4Å: Chain A: Q.143, G.144, L.145, P.146 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.143 Water bridges: A:L.147 EDO.9: 6 residues within 4Å: Chain A: I.137, Y.142, E.287, G.291, D.292, Y.293 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.287 EDO.10: 4 residues within 4Å: Chain A: E.354, V.355, E.358, K.359 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.359 Water bridges: A:E.354 EDO.11: 8 residues within 4Å: Chain A: E.85, L.89, V.106, F.126, A.240, D.241, L.242 Ligands: W4A.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.241, A:L.242 EDO.12: 3 residues within 4Å: Chain A: S.91, N.94, S.95 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.94, A:C.168, A:W.247 EDO.13: 7 residues within 4Å: Chain A: F.286, Y.293, L.294, W.350, V.355, K.359, Y.360 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.294, A:K.359, A:K.359

4 x CA: CALCIUM ION(Non-covalent)

CA.14: 3 residues within 4Å: Chain A: E.358, E.361 Ligands: CA.15 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.358, A:E.361, A:E.361 CA.15: 2 residues within 4Å: Chain A: E.361 Ligands: CA.14 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.361, H2O.3, H2O.7 CA.16: 2 residues within 4Å: Chain A: E.354, E.358 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.354, A:E.358, A:E.358, H2O.7, H2O.8 CA.17: 1 residues within 4Å: Chain A: E.354 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.354, A:E.354, H2O.8

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.18: 4 residues within 4Å: Chain A: E.296, H.298, D.308, L.312 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.308 Water bridges: A:Y.303, A:Y.303

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

2017-05-24

Peptides

SRPK1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

SRPK1