6HVD - chain A (model A) | STE20 like kinase
Structure information
| PDB: | 6HVD |
| PubMed: | - |
| Release date: | 2018-10-17 |
| Resolution: | 1.63 Å |
| Kinase: | SLK |
| Family: | STE20 |
| Group: | STE |
| Species: | HUMAN |
| Quality Score: | 8.7 |
| Missing Residues: | 0 |
| Missing Atoms: | 13 |
| DFG conformation: | in |
| αC-helix conformation: | in |
| Salt bridge KIII.17 and EαC.24: | Yes (2.9Å) |
| ASP rotation (xDFG.81) : | 353° |
| PHE rotation (xDFG.82) : | 15° |
| Activation loop position: | -3.4Å |
| αC-helix position: | 18.1Å |
| G-rich loop angle: | 55.8° |
| G-rich loop distance: | 16.5Å |
| G-rich loop rotation: | 70.4° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond protein
I2
H-bond protein
I4
H-bond protein
I5
H-bond ligand
H-bond protein
I7
No H-bonds
Binding pocket sequence
| Uniprot | GELGDGAFGKVYKAAAKVIDYMVEIDILASCDPNIVKLLDAWILIEFCAGGAVDAVMLEYLHDNKIIHRDLKAGNILFLADFGVS |
| Structure: | GELGDGAFGKVYKAAAKVIDYMVEIDILASCDPNIVKLLDAWILIEFCAGGAVDAVMLEYLHDNKIIHRDLKAGNILFLADFGVS |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: GUQ
Ligand Name: 3-(1,3-benzothiazol-2-ylamino)-4-(2-methoxyphenyl)pyrrole-2,5-dione
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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 G 38 | 2 E 39 | 3 L 40 | 4 G 41 | 5 D 42 | 6 G 43 | 7 A 44 | 8 F 45 | 9 G 46 | 10 K 47 | 11 V 48 | 12 Y 49 | 13 K 50 | 14 A 60 | 15 A 61 | 16 A 62 | 17 K 63 | 18 V 64 | 19 I 65 | 20 D 75 |
| ■ | ■ | ■ | ■ | ■ | ■ | ||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 Y 76 | 22 M 77 | 23 V 78 | 24 E 79 | 25 I 80 | 26 D 81 | 27 I 82 | 28 L 83 | 29 A 84 | 30 S 85 | 31 C 86 | 32 D 87 | 33 P 89 | 34 N 90 | 35 I 91 | 36 V 92 | 37 K 93 | 38 L 94 | 39 L 95 | 40 D 96 |
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 A 97 | 42 W 105 | 43 I 106 | 44 L 107 | 45 I 108 | 46 E 109 | 47 F 110 | 48 C 111 | 49 A 112 | 50 G 113 | 51 G 114 | 52 A 115 | 53 V 116 | 54 D 117 | 55 A 118 | 56 V 119 | 57 M 120 | 58 L 121 | 59 E 122 | 60 Y 145 |
| ■ | ▲ | ■ | ▲ | ||||||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 L 146 | 62 H 147 | 63 D 148 | 64 N 149 | 65 K 150 | 66 I 151 | 67 I 152 | 68 H 153 | 69 R 154 | 70 D 155 | 71 L 156 | 72 K 157 | 73 A 158 | 74 G 159 | 75 N 160 | 76 I 161 | 77 L 162 | 78 F 163 | 79 L 171 | 80 A 172 |
| ■ | ■ | ■ | ■ | ||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 173 | 82 F 174 | 83 G 175 | 84 V 176 | 85 S 177 | |||||||||||||||
| ■ | |||||||||||||||||||
Binding affinities
Ligand not found in ChEMBL.