6CFM - chain B (model B) | Vaccinia related kinase 1
Structure information
PDB: | 6CFM |
PubMed: | - |
Release date: | 2018-03-07 |
Resolution: | 2.45 Å |
Kinase: | VRK1 |
Family: | VRK |
Group: | CK1 |
Species: | HUMAN |
Quality Score: | 5.2 |
Missing Residues: | 7 |
Missing Atoms: | 20 |
DFG conformation: | in |
αC-helix conformation: | in |
Salt bridge KIII.17 and EαC.24: | Yes (2.9Å) |
ASP rotation (xDFG.81) : | 345° |
PHE rotation (xDFG.82) : | 11° |
Activation loop position: | -3.7Å |
αC-helix position: | 17.5Å |
G-rich loop angle: | - |
G-rich loop distance: | - |
G-rich loop rotation: | - |
Other models from this PDB:
2D & 3D views
Binding pocket waters
No waters were found in the defined clusters
Binding pocket sequence
Uniprot | LPIGQGGFGCIYLCVVKVEPLFTELKFYQRAALGVPKYWGSFMIMDRFG-SDLQKIYEAYIHEHEYVHGDIKASNLLLLVDYGLA |
Structure: | LP_______CIYLCVVKVEPLFTELKFYQRAALGVPKYWGSFMIMDRFG_SDLQKIYEAYIHEHEYVHGDIKASNLLLLVDYGLA |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: EA7
Ligand Name: (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7-dimethyl-8-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one
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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 L 41 | 2 P 42 | 3 _ _ | 4 _ _ | 5 _ _ | 6 _ _ | 7 _ _ | 8 _ _ | 9 _ _ | 10 C 50 | 11 I 51 | 12 Y 52 | 13 L 53 | 14 C 68 | 15 V 69 | 16 V 70 | 17 K 71 | 18 V 72 | 19 E 73 | 20 P 79 |
■ | ■ | ■▲ | |||||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 L 80 | 22 F 81 | 23 T 82 | 24 E 83 | 25 L 84 | 26 K 85 | 27 F 86 | 28 Y 87 | 29 Q 88 | 30 R 89 | 31 A 90 | 32 A 91 | 33 L 108 | 34 G 109 | 35 V 110 | 36 P 111 | 37 K 112 | 38 Y 113 | 39 W 114 | 40 G 115 |
▲ | ■ | ||||||||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 S 116 | 42 F 128 | 43 M 129 | 44 I 130 | 45 M 131 | 46 D 132 | 47 R 133 | 48 F 134 | 49 G 135 | 50 _ _ | 51 S 136 | 52 D 137 | 53 L 138 | 54 Q 139 | 55 K 140 | 56 I 141 | 57 Y 142 | 58 E 143 | 59 A 144 | 60 Y 167 |
■ | ▲ | ■ | ■♦▲ | ■ | ■ | ||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 I 168 | 62 H 169 | 63 E 170 | 64 H 171 | 65 E 172 | 66 Y 173 | 67 V 174 | 68 H 175 | 69 G 176 | 70 D 177 | 71 I 178 | 72 K 179 | 73 A 180 | 74 S 181 | 75 N 182 | 76 L 183 | 77 L 184 | 78 L 185 | 79 L 195 | 80 V 196 |
■ | ■ | ||||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 197 | 82 Y 198 | 83 G 199 | 84 L 200 | 85 A 201 | |||||||||||||||
■▲ |
Binding affinities
Ligand not found in ChEMBL.