SMTL ID : 6yu1.2 (1 other biounit)

CLK3 bound with beta-carboline KH-CARB13 (Cpd 3)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: L.288, V.289, W.290 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.290 EDO.2: 6 residues within 4Å: Chain A: S.1, M.2, I.24, G.25, E.33, V.35 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.2, A:E.33 Water bridges: A:S.1, A:Q.3 EDO.6: 3 residues within 4Å: Chain A: T.213, H.215 Ligands: EDO.12 No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain A: E.263, K.264, E.292 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.264 Water bridges: A:K.264 EDO.8: 5 residues within 4Å: Chain A: S.8, S.11, V.21, D.26, W.27 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.21, A:W.27, A:W.27 EDO.9: 6 residues within 4Å: Chain A: G.226, W.227, A.228, P.230, P.333 Ligands: EDO.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.228 Water bridges: A:E.220 EDO.10: 7 residues within 4Å: Chain A: R.327, A.334, Q.335, R.336, I.337, T.338, E.341 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.327, A:Q.335 Water bridges: A:R.327 EDO.11: 4 residues within 4Å: Chain A: E.317, Q.320, P.346, A.349 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.320 Water bridges: A:G.350 EDO.12: 7 residues within 4Å: Chain A: F.120, K.161, P.162, E.163, Y.216 Ligands: EDO.6, EDO.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.163 EDO.13: 2 residues within 4Å: Chain A: F.120 Ligands: EDO.12 No protein-ligand interaction detected (PLIP) EDO.14: 4 residues within 4Å: Chain A: H.275, R.276, T.277, R.278 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.275 EDO.15: 6 residues within 4Å: Chain A: E.263, P.268, I.274, G.286, G.287, L.288 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.288 EDO.16: 6 residues within 4Å: Chain A: C.22, I.24, N.37, E.40, K.45, V.47 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.37, A:E.40, A:K.45 Water bridges: A:C.22 EDO.17: 4 residues within 4Å: Chain A: H.207, G.226, W.227 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.227, A:W.227 EDO.18: 8 residues within 4Å: Chain A: F.247, T.248, L.249, F.250, Q.251, N.303, C.304, Y.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.251, A:Q.251

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 5 residues within 4Å: Chain A: N.255, R.278, K.279, K.281, Y.282 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.278, A:R.278, A:K.279, A:K.281 Water bridges: A:Y.282 PG4.5: 4 residues within 4Å: Chain A: N.66, V.67, G.68, R.71 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.68, A:R.71, A:R.71 Water bridges: A:K.69

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

PO4.4: 3 residues within 4Å: Chain A: R.65, K.69, Y.70 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.70 Water bridges: A:K.69 Salt bridges: A:R.65, A:K.69

1 x KHC: (4~{S})-7,8-bis(chloranyl)-9-methyl-1-oxidanylidene-spiro[2,4-dihydropyrido[3,4-b]indole-3,4'-piperidine]-4-carbonitrile(Non-covalent)

KHC.19: 11 residues within 4Å: Chain A: L.38, V.46, A.60, K.62, F.112, L.114, L.115, G.116, K.117, N.118, L.166 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.38, A:V.46, A:L.114 Hydrogen bonds: A:L.115, A:L.115, A:N.118 Water bridges: A:N.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schroder, M. et al., DFG-1 Residue Controls Inhibitor Binding Mode and Affinity, Providing a Basis for Rational Design of Kinase Inhibitor Selectivity. J.Med.Chem. (2020)

Release Date

2020-07-15

Peptides

Dual specificity protein kinase CLK3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
c

Dual specificity protein kinase CLK3

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