5DBX - chain A (model A) | Serine/threonine kinase 39
Structure information
PDB: | 5DBX |
PubMed: | 26208601 |
Release date: | 2015-09-23 |
Resolution: | 2.5 Å |
Kinase: | Stk39 (STLK3) |
Family: | STE20 |
Group: | STE |
Species: | MOUSE |
Quality Score: | 7.6 |
Missing Residues: | 1 |
Missing Atoms: | 0 |
DFG conformation: | in |
αC-helix conformation: | out |
Salt bridge KIII.17 and EαC.24: | No (17.4Å) |
ASP rotation (xDFG.81) : | ° |
PHE rotation (xDFG.82) : | 180° |
Activation loop position: | -4.4Å |
αC-helix position: | 24.5Å |
G-rich loop angle: | 56.7° |
G-rich loop distance: | 16.8Å |
G-rich loop rotation: | 42.8° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
No waters were found in the defined clusters
Binding pocket sequence
Uniprot | EVIGSGATAVVQAVAIKRIELLKEIQAMSQCSPNVVTYYTSWLVMKLLSGGSMLDIIKYYLHRNGQIHRDLKAGNILLIADFGVS |
Structure: | EVIGSGATAVVQAVAIKRIELLKEIQAMSQ_SPNVVTYYTSWLVMKLLSGGSMLDIIKYYLHRNGQIHRDLKAGNILLIADFGVS |
Modified residues
No modified residues identified.
Orthosteric ligand
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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 E 79 | 2 V 80 | 3 I 81 | 4 G 82 | 5 S 83 | 6 G 84 | 7 A 85 | 8 T 86 | 9 A 87 | 10 V 88 | 11 V 89 | 12 Q 90 | 13 A 91 | 14 V 101 | 15 A 102 | 16 I 103 | 17 K 104 | 18 R 105 | 19 I 106 | 20 E 117 |
■ | ■ | ■ | ■ | ■ | ▲ | ||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 L 118 | 22 L 119 | 23 K 120 | 24 E 121 | 25 I 122 | 26 Q 123 | 27 A 124 | 28 M 125 | 29 S 126 | 30 Q 127 | 31 _ _ | 32 S 129 | 33 P 131 | 34 N 132 | 35 V 133 | 36 V 134 | 37 T 135 | 38 Y 136 | 39 Y 137 | 40 T 138 |
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 S 139 | 42 W 147 | 43 L 148 | 44 V 149 | 45 M 150 | 46 K 151 | 47 L 152 | 48 L 153 | 49 S 154 | 50 G 155 | 51 G 156 | 52 S 157 | 53 M 158 | 54 L 159 | 55 D 160 | 56 I 161 | 57 I 162 | 58 K 163 | 59 Y 164 | 60 Y 194 |
■ | ▲ | ■ | ■▲ | ||||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 L 195 | 62 H 196 | 63 R 197 | 64 N 198 | 65 G 199 | 66 Q 200 | 67 I 201 | 68 H 202 | 69 R 203 | 70 D 204 | 71 L 205 | 72 K 206 | 73 A 207 | 74 G 208 | 75 N 209 | 76 I 210 | 77 L 211 | 78 L 212 | 79 I 220 | 80 A 221 |
■ | |||||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 222 | 82 F 223 | 83 G 224 | 84 V 225 | 85 S 226 | |||||||||||||||
Binding affinities
ChEMBL ID:CHEMBL1230989Bioaffinities: No (p)Ki/(p)IC50/(p)EC50 values for kinases found (with a ChEMBL confidence ≥ 8).