5UU1 - chain A | Vaccinia related kinase 2
Structure information
PDB: | 5UU1 |
PubMed: | 28790404 |
Release date: | 2017-03-01 |
Resolution: | 2 Å |
Kinase: | VRK2 |
Family: | VRK |
Group: | CK1 |
Species: | HUMAN |
Quality Score: | 8.2 |
Missing Residues: | 0 |
Missing Atoms: | 18 |
DFG conformation: | in |
αC-helix conformation: | in |
Salt bridge KIII.17 and EαC.24: | Yes (2.7Å) |
ASP rotation (xDFG.81) : | 6° |
PHE rotation (xDFG.82) : | 13° |
Activation loop position: | -4.8Å |
αC-helix position: | 18Å |
G-rich loop angle: | 53° |
G-rich loop distance: | 15.3Å |
G-rich loop rotation: | 64.3° |
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond ligand
H-bond protein
I5
H-bond ligand
H-bond protein
Binding pocket sequence
Uniprot | KKIGSGGFGLIYLHVVKVEPLFSELKFYQRVALGIPLFYGSFMVMERLG-IDLQKISGQYIHENEYVHGDIKAANLLLLADYGLS |
Structure: | KKIGSGGFGLIYLHVVKVEPLFSELKFYQRVALGIPLFYGSFMVMERLG_IDLQKISGQYIHENEYVHGDIKAANLLLLADYGLS |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: 7DZ
Ligand Name: (7S)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7-dimethyl-8-(3-methylbutyl)-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 K 33 | 2 K 34 | 3 I 35 | 4 G 36 | 5 S 37 | 6 G 38 | 7 G 39 | 8 F 40 | 9 G 41 | 10 L 42 | 11 I 43 | 12 Y 44 | 13 L 45 | 14 H 58 | 15 V 59 | 16 V 60 | 17 K 61 | 18 V 62 | 19 E 63 | 20 P 69 |
■ | ■ | ■ | ■ | ■ | ■▲ | ||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 L 70 | 22 F 71 | 23 S 72 | 24 E 73 | 25 L 74 | 26 K 75 | 27 F 76 | 28 Y 77 | 29 Q 78 | 30 R 79 | 31 V 80 | 32 A 81 | 33 L 98 | 34 G 99 | 35 I 100 | 36 P 101 | 37 L 102 | 38 F 103 | 39 Y 104 | 40 G 105 |
■ | ■ | ||||||||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 S 106 | 42 F 118 | 43 M 119 | 44 V 120 | 45 M 121 | 46 E 122 | 47 R 123 | 48 L 124 | 49 G 125 | 50 _ _ | 51 I 126 | 52 D 127 | 53 L 128 | 54 Q 129 | 55 K 130 | 56 I 131 | 57 S 132 | 58 G 133 | 59 Q 134 | 60 Y 156 |
■ | ▲ | ■ | ■▲ | ■ | |||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 I 157 | 62 H 158 | 63 E 159 | 64 N 160 | 65 E 161 | 66 Y 162 | 67 V 163 | 68 H 164 | 69 G 165 | 70 D 166 | 71 I 167 | 72 K 168 | 73 A 169 | 74 A 170 | 75 N 171 | 76 L 172 | 77 L 173 | 78 L 174 | 79 L 184 | 80 A 185 |
■ | ■ | ■ | |||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 186 | 82 Y 187 | 83 G 188 | 84 L 189 | 85 S 190 | |||||||||||||||
■ |
Binding affinities
Ligand not found in ChEMBL.