3UBD - chain A (model A) | Ribosomal protein S6 kinase polypeptide 3
Structure information
PDB: | 3UBD |
PubMed: | 22846040 |
Release date: | 2012-09-05 |
Resolution: | 1.53 Å |
Kinase: | Rps6ka3 (RSK2) |
Family: | RSK |
Group: | AGC |
Species: | MOUSE |
Quality Score: | 3.6 |
Missing Residues: | 6 |
Missing Atoms: | 0 |
DFG conformation: | out-like |
αC-helix conformation: | na |
Salt bridge KIII.17 and EαC.24: | NA |
ASP rotation (xDFG.81) : | 109° |
PHE rotation (xDFG.82) : | 203° |
Activation loop position: | -2.1Å |
αC-helix position: | 0Å |
G-rich loop angle: | 76.2° |
G-rich loop distance: | 22.1Å |
G-rich loop rotation: | 57.9° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
No waters were found in the defined clusters
Binding pocket sequence
Uniprot | KVLGQGSFGKVFLYAMKVLRTKMERDILVEVNPFIVKLHYAYLILDFLRGGDLFTRLSKHLHSLGIIYRDLKPENILLLTDFGLS |
Structure: | KVLGQGSFGKVFLYAMKVL______DILVEVNPFIVKLHYAYLILDFLRGGDLFTRLSKHLHSLGIIYRDLKPENILLLTDFGLS |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: SL0
Ligand Name: 5,7-dihydroxy-2-(4-hydroxyphenyl)-4-oxo-4H-chromen-3-yl 3,4-di-O-acetyl-6-deoxy-alpha-L-mannopyranoside
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- LABELS
- KLIFS residue #
- Amino Acid
- None
- COLORS
- Interaction types
- KLIFS (all res.)
- KLIFS (interacting res.)
- None
- OTHER
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This ligand targets the following (sub)pockets:
Main pockets | |
---|---|
Front | |
Gate | |
Back |
Subpockets | |
---|---|
FP-I | |
FP-II | |
BP-I-A | |
BP-I-B | |
BP-II-in | |
BP-II-A-in | |
BP-II-B-in | |
BP-II-out | |
BP-II-B | |
BP-III | |
BP-IV | |
BP-V |
Kinase-ligand interactions
■ Hydrophobic ♦ Aromatic face-to-face ♦ Aromatic face-to-edge ▲ H-bond donor ▲ H-bond acceptor ● Ionic positive ● Ionic negative
I | g.l | II | III | αC | |||||||||||||||
1 K 72 | 2 V 73 | 3 L 74 | 4 G 75 | 5 Q 76 | 6 G 77 | 7 S 78 | 8 F 79 | 9 G 80 | 10 K 81 | 11 V 82 | 12 F 83 | 13 L 84 | 14 Y 97 | 15 A 98 | 16 M 99 | 17 K 100 | 18 V 101 | 19 L 102 | 20 _ _ |
■♦ | ■ | ■ | ■ | ||||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 _ _ | 22 _ _ | 23 _ _ | 24 _ _ | 25 _ _ | 26 D 120 | 27 I 121 | 28 L 122 | 29 V 123 | 30 E 124 | 31 V 125 | 32 N 126 | 33 P 128 | 34 F 129 | 35 I 130 | 36 V 131 | 37 K 132 | 38 L 133 | 39 H 134 | 40 Y 135 |
■ | |||||||||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 A 136 | 42 Y 144 | 43 L 145 | 44 I 146 | 45 L 147 | 46 D 148 | 47 F 149 | 48 L 150 | 49 R 151 | 50 G 152 | 51 G 153 | 52 D 154 | 53 L 155 | 54 F 156 | 55 T 157 | 56 R 158 | 57 L 159 | 58 S 160 | 59 K 161 | 60 H 183 |
■ | ■ | ■▲ | ■ | ■ | |||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 L 184 | 62 H 185 | 63 S 186 | 64 L 187 | 65 G 188 | 66 I 189 | 67 I 190 | 68 Y 191 | 69 R 192 | 70 D 193 | 71 L 194 | 72 K 195 | 73 P 196 | 74 E 197 | 75 N 198 | 76 I 199 | 77 L 200 | 78 L 201 | 79 L 209 | 80 T 210 |
▲ | ■ | ■ | |||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 211 | 82 F 212 | 83 G 213 | 84 L 214 | 85 S 215 | |||||||||||||||
■ | ■ |
Binding affinities
ChEMBL ID:CHEMBL240954Bioaffinities: 10 records for 1 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Ribosomal protein S6 kinase alpha 3 | 6.4 | 6 | 7.1 | pIC50 | 10 |