SMTL ID : 7zkx.1

SRPK2 IN COMPLEX WITH INHIBITOR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

monomer

Ligands

1 x IXQ: N-[3-[[[2-(6-chloranyl-5-fluoranyl-1H-benzimidazol-2-yl)pyrimidin-4-yl]amino]methyl]pyridin-2-yl]-N-methyl-methanesulfonamide(Non-covalent)

IXQ.1: 19 residues within 4Å: Chain A: L.18, G.19, W.20, G.21, V.26, A.39, F.97, E.98, V.99, L.100, G.101, H.102, H.103, E.149, L.152, Y.159, M.163, D.461 Ligands: ACT.11 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.18, A:L.18, A:F.97, A:L.152 Hydrogen bonds: A:L.100, A:G.101 Water bridges: A:H.103

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

SO4.2: 4 residues within 4Å: Chain A: R.552, N.556, R.557, R.562 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.557 Water bridges: A:R.552, A:N.556, A:R.557, A:R.557 Salt bridges: A:R.552, A:R.557, A:R.562 SO4.3: 3 residues within 4Å: Chain A: R.479, R.482, R.525 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.479 Salt bridges: A:R.479, A:R.482, A:R.525 SO4.4: 4 residues within 4Å: Chain A: S.607, G.609, E.610, R.613 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.607, A:S.607 Water bridges: A:G.609 Salt bridges: A:R.613 SO4.5: 3 residues within 4Å: Chain A: S.519, S.524, R.525 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.525, A:R.525 Water bridges: A:D.526 SO4.12: 4 residues within 4Å: Chain A: E.516, H.518, D.528, H.532 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.516, A:H.518 Water bridges: A:H.518 Salt bridges: A:H.518, A:H.532

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

EDO.6: 3 residues within 4Å: Chain A: Y.513, L.514, V.575 No protein-ligand interaction detected (PLIP) EDO.8: 5 residues within 4Å: Chain A: D.70, N.72, D.133, Y.134, K.138 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.72, A:D.133, A:K.138 EDO.9: 6 residues within 4Å: Chain A: D.145, N.464, D.475, I.476, Q.477, R.482 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.145, A:D.475, A:Q.477, A:R.482

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.7: 3 residues within 4Å: Chain A: H.518, S.519, R.525 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.519 Water bridges: A:P.517, A:R.525 NO3.10: 5 residues within 4Å: Chain A: R.119, K.122, S.123, R.126, D.453 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.126, A:R.126, A:D.453

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

ACT.11: 7 residues within 4Å: Chain A: K.41, E.56, V.77, F.97, A.460, D.461 Ligands: IXQ.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.77, A:F.97 Hydrogen bonds: A:D.461, A:D.461 Water bridges: A:L.462 Salt bridges: A:K.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schroder, M. et al., MSC-1186, a Highly Selective Pan-SRPK Inhibitor Based on an Exceptionally Decorated Benzimidazole-Pyrimidine Core. J.Med.Chem. (2023)

Release Date

2023-02-22

Peptides

SRSF protein kinase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

SRSF protein kinase 2