3LM0 - chain A (model B) | Serine/threonine kinase 17b
Structure information
| PDB: | 3LM0 |
| PubMed: | - |
| Release date: | 2010-03-16 |
| Resolution: | 2.35 Å |
| Kinase: | STK17B (DRAK2) |
| Family: | DAPK |
| Group: | CAMK |
| Species: | HUMAN |
| Quality Score: | 9.3 |
| Missing Residues: | 0 |
| Missing Atoms: | 7 |
| DFG conformation: | in |
| αC-helix conformation: | in |
| Salt bridge KIII.17 and EαC.24: | Yes (3.5Å) |
| ASP rotation (xDFG.81) : | 347° |
| PHE rotation (xDFG.82) : | 8° |
| Activation loop position: | -3.6Å |
| αC-helix position: | 17.9Å |
| G-rich loop angle: | 53.8° |
| G-rich loop distance: | 16.3Å |
| G-rich loop rotation: | 40.5° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond protein
Binding pocket sequence
| Uniprot | KELGRGKFAVVRQYAAKFLEILHEIAVLELAKPRVINLHEVILILEYAAGGEIFSLCLPYLHQNNIVHLDLKPQNILLIVDFGMS |
| Structure: | KELGRGKFAVVRQYAAKFLEILHEIAVLELAKPRVINLHEVILILEYAAGGEIFSLCLPYLHQNNIVHLDLKPQNILLIVDFGMS |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: EBD
Ligand Name: [4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]-5-methylpyrimidin-2-yl}amino)phenyl]acetonitrile
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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 K 37 | 2 E 38 | 3 L 39 | 4 G 40 | 5 R 41 | 6 G 42 | 7 K 43 | 8 F 44 | 9 A 45 | 10 V 46 | 11 V 47 | 12 R 48 | 13 Q 49 | 14 Y 59 | 15 A 60 | 16 A 61 | 17 K 62 | 18 F 63 | 19 L 64 | 20 E 76 |
| ■ | ■ | ■ | ■▲ | ||||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 I 77 | 22 L 78 | 23 H 79 | 24 E 80 | 25 I 81 | 26 A 82 | 27 V 83 | 28 L 84 | 29 E 85 | 30 L 86 | 31 A 87 | 32 K 88 | 33 P 91 | 34 R 92 | 35 V 93 | 36 I 94 | 37 N 95 | 38 L 96 | 39 H 97 | 40 E 98 |
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 V 99 | 42 I 107 | 43 L 108 | 44 I 109 | 45 L 110 | 46 E 111 | 47 Y 112 | 48 A 113 | 49 A 114 | 50 G 115 | 51 G 116 | 52 E 117 | 53 I 118 | 54 F 119 | 55 S 120 | 56 L 121 | 57 C 122 | 58 L 123 | 59 P 124 | 60 Y 148 |
| ■ | ▲ | ■♦ | ■▲ | ■ | ■ | ■▲ | |||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 L 149 | 62 H 150 | 63 Q 151 | 64 N 152 | 65 N 153 | 66 I 154 | 67 V 155 | 68 H 156 | 69 L 157 | 70 D 158 | 71 L 159 | 72 K 160 | 73 P 161 | 74 Q 162 | 75 N 163 | 76 I 164 | 77 L 165 | 78 L 166 | 79 I 177 | 80 V 178 |
| ■ | ■ | ■ | |||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 179 | 82 F 180 | 83 G 181 | 84 M 182 | 85 S 183 | |||||||||||||||
| ■ | |||||||||||||||||||
Binding affinities
Ligand not found in ChEMBL.