SMTL ID : 6z55.1 (1 other biounit)

Crystal structure of CLK3 in complex with macrocycle ODS2004070

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

PO4.1: 1 residues within 4Å: Chain A: T.209 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.209, A:T.209 PO4.2: 2 residues within 4Å: Chain A: R.278, K.281 10 PLIP interactions: 10 interactions with chain A Water bridges: A:R.278, A:R.278, A:R.278, A:R.278, A:R.278, A:K.281, A:K.281, A:K.281 Salt bridges: A:R.278, A:K.281 PO4.3: 3 residues within 4Å: Chain A: R.65, K.69, Y.70 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.70 Salt bridges: A:R.65, A:K.69

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

EDO.4: 3 residues within 4Å: Chain A: L.288, V.289, W.290 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.290 Water bridges: A:W.290 EDO.5: 6 residues within 4Å: Chain A: R.327, A.334, Q.335, R.336, I.337, E.341 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.327, A:Q.335 Water bridges: A:R.327 EDO.6: 7 residues within 4Å: Chain A: F.247, T.248, L.249, I.265, N.303, C.304, Y.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.248 Water bridges: A:Q.251, A:Y.310 EDO.7: 1 residues within 4Å: Chain A: G.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.68 Water bridges: A:K.69 EDO.8: 2 residues within 4Å: Chain A: E.224, R.278 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.224, A:R.278 Water bridges: A:T.209 EDO.9: 7 residues within 4Å: Chain A: S.8, S.11, V.21, C.22, D.26, W.27 Ligands: NA.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.21, A:W.27, A:W.27 EDO.10: 2 residues within 4Å: Chain A: Q.29, E.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.30 EDO.11: 5 residues within 4Å: Chain A: R.75, I.78, N.79, K.82, W.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.75, A:K.82, A:K.82 EDO.12: 4 residues within 4Å: Chain A: G.198, S.199, A.200, T.208 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.200, A:T.208 Water bridges: A:A.200 EDO.13: 2 residues within 4Å: Chain A: E.171, F.172 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.172 Water bridges: A:S.170 EDO.14: 1 residues within 4Å: Chain A: R.298 No protein-ligand interaction detected (PLIP) EDO.15: 3 residues within 4Å: Chain A: S.294, S.295, D.296 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.294, A:S.295, A:D.296 Water bridges: A:S.294, A:S.295 EDO.16: 3 residues within 4Å: Chain A: E.205, H.206, H.207 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.205, A:H.206, A:H.207

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

NA.17: 7 residues within 4Å: Chain A: Q.154, L.155, T.156, T.201, F.202, D.203, Q.229 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.154, A:T.156, A:Q.229 NA.18: 3 residues within 4Å: Chain A: S.8, S.11 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.8

1 x PQ5: 7,10-Dioxa-13,17,18,21-tetrazatetracyclo[12.5.2.12,6.017,20]docosa-1(20),2(22),3,5,14(21),15,18-heptaene-5-carboxylic acid(Non-covalent)

PQ5.19: 12 residues within 4Å: Chain A: L.38, V.46, A.60, K.62, V.96, F.112, E.113, L.114, L.115, L.166, A.195, D.196 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.60, A:F.112, A:L.166, A:A.195 Hydrogen bonds: A:L.38, A:L.115, A:D.196 Water bridges: A:K.62, A:F.197, A:F.197 Salt bridges: A:K.62 pi-Stacking: A:F.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaikuad, A. et al., Crystal structure of CLK3 in complex with macrocycle ODS2004070. To Be Published

Release Date

2020-06-03

Peptides

Dual specificity protein kinase CLK3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dual specificity protein kinase CLK3

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