4L45 - chain A | Ribosomal protein S6 kinase B1
Structure information
PDB: | 4L45 |
PubMed: | 23731517 |
Release date: | 2013-07-24 |
Resolution: | 2.9 Å |
Kinase: | RPS6KB1 (p70S6K) |
Family: | RSK |
Group: | AGC |
Species: | HUMAN |
Quality Score: | 8 |
Missing Residues: | 0 |
Missing Atoms: | 0 |
DFG conformation: | in |
αC-helix conformation: | in |
Salt bridge KIII.17 and EαC.24: | Yes (2.8Å) |
ASP rotation (xDFG.81) : | 355° |
PHE rotation (xDFG.82) : | 17° |
Activation loop position: | -3.1Å |
αC-helix position: | 17.7Å |
G-rich loop angle: | 61.6° |
G-rich loop distance: | 19.4Å |
G-rich loop rotation: | 50.1° |
2D & 3D views
Binding pocket waters
No waters were found in the defined clusters
Binding pocket sequence
Uniprot | RVLGKGGYGKVFQFAMKVLHTKAERNILEEVKPFIVDLIYAYLILEYLSGGELFMQLERHLHQKGIIYRDLKPENIMLLTDFGLC |
Structure: | RVLGKGGYGKVFQFAMKVLHTKAERNILEEVKPFIVDLIYAYLILEYLSGGELFMQLERHLHQKGIIYRDLKPENIMLLTDFGLC |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: 5FI
Ligand Name: 2-{[4-(5-ethylpyrimidin-4-yl)piperazin-1-yl]methyl}-5-(trifluoromethyl)-1H-benzimidazole
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- LABELS
- KLIFS residue #
- Amino Acid
- None
- COLORS
- Interaction types
- KLIFS (all res.)
- KLIFS (interacting res.)
- None
- OTHER
- Show/hide non-interacting res.
- En/disable resizing interacting res.
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 R 72 | 2 V 73 | 3 L 74 | 4 G 75 | 5 K 76 | 6 G 77 | 7 G 78 | 8 Y 79 | 9 G 80 | 10 K 81 | 11 V 82 | 12 F 83 | 13 Q 84 | 14 F 97 | 15 A 98 | 16 M 99 | 17 K 100 | 18 V 101 | 19 L 102 | 20 H 116 |
■ | ■ | ■ | ■ | ■ | ■ | ■ | ■ | ■ | ■ | ||||||||||
αC | b.l | IV | |||||||||||||||||
21 T 117 | 22 K 118 | 23 A 119 | 24 E 120 | 25 R 121 | 26 N 122 | 27 I 123 | 28 L 124 | 29 E 125 | 30 E 126 | 31 V 127 | 32 K 128 | 33 P 130 | 34 F 131 | 35 I 132 | 36 V 133 | 37 D 134 | 38 L 135 | 39 I 136 | 40 Y 137 |
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 A 138 | 42 Y 146 | 43 L 147 | 44 I 148 | 45 L 149 | 46 E 150 | 47 Y 151 | 48 L 152 | 49 S 153 | 50 G 154 | 51 G 155 | 52 E 156 | 53 L 157 | 54 F 158 | 55 M 159 | 56 Q 160 | 57 L 161 | 58 E 162 | 59 R 163 | 60 H 185 |
■ | ■ | ■♦ | ■▲ | ||||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 L 186 | 62 H 187 | 63 Q 188 | 64 K 189 | 65 G 190 | 66 I 191 | 67 I 192 | 68 Y 193 | 69 R 194 | 70 D 195 | 71 L 196 | 72 K 197 | 73 P 198 | 74 E 199 | 75 N 200 | 76 I 201 | 77 M 202 | 78 L 203 | 79 L 211 | 80 T 212 |
■ | ■ | ||||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 213 | 82 F 214 | 83 G 215 | 84 L 216 | 85 C 217 | |||||||||||||||
■ | ■ |
Binding affinities
ChEMBL ID:CHEMBL2134202Bioaffinities: 2 records for 1 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Ribosomal protein S6 kinase 1 | 6.8 | 6.8 | 6.8 | pIC50 | 1 |
Homo sapiens | Ribosomal protein S6 kinase 1 | 7.7 | 7.7 | 7.7 | pKi | 1 |