5ZXB - chain A (model B) | Tyrosine kinase, non-receptor, 2
Structure information
PDB: | 5ZXB |
PubMed: | 30153003 |
Release date: | 2018-09-26 |
Resolution: | 2.2 Å |
Kinase: | TNK2 (ACK) |
Family: | Ack |
Group: | TK |
Species: | HUMAN |
Quality Score: | 5.6 |
Missing Residues: | 6 |
Missing Atoms: | 0 |
DFG conformation: | out |
αC-helix conformation: | in |
Salt bridge KIII.17 and EαC.24: | Yes (2.6Å) |
ASP rotation (xDFG.81) : | 186° |
PHE rotation (xDFG.82) : | 177° |
Activation loop position: | 2.3Å |
αC-helix position: | 19.2Å |
G-rich loop angle: | - |
G-rich loop distance: | - |
G-rich loop rotation: | - |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond ligand
H-bond protein
O1
H-bond ligand
Binding pocket sequence
Uniprot | EKLGDGSFGVVRRVAVKCLDFIREVNAMHSLDRNLIRLYGVKMVTELAPLGSLLDRLRKYLESKRFIHRDLAARNLLLIGDFGLM |
Structure: | EKLGD___GVVRRVAVKCLDFIREVNAMHSLDRNLIRLYGVKMVTELAPLGSLLDRLRKYLESKRFIHRDLAARNLLLIGDF___ |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: 9KO
Ligand Name: N-{3-[7-{[6-(4-acetylpiperazin-1-yl)pyridin-3-yl]amino}-1-methyl-2-oxo-1,4-dihydropyrimido[4,5-d]pyrimidin-3(2H)-yl]-4-methylphenyl}-3-(trifluoromethyl)benzamide
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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 130 | 2 K 131 | 3 L 132 | 4 G 133 | 5 D 134 | 6 _ _ | 7 _ _ | 8 _ _ | 9 G 138 | 10 V 139 | 11 V 140 | 12 R 141 | 13 R 142 | 14 V 155 | 15 A 156 | 16 V 157 | 17 K 158 | 18 C 159 | 19 L 160 | 20 D 173 |
■ | ■ | ■ | ■ | ■ | |||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 F 174 | 22 I 175 | 23 R 176 | 24 E 177 | 25 V 178 | 26 N 179 | 27 A 180 | 28 M 181 | 29 H 182 | 30 S 183 | 31 L 184 | 32 D 185 | 33 R 187 | 34 N 188 | 35 L 189 | 36 I 190 | 37 R 191 | 38 L 192 | 39 Y 193 | 40 G 194 |
■▲ | ■ | ■ | ■ | ■ | |||||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 V 195 | 42 K 202 | 43 M 203 | 44 V 204 | 45 T 205 | 46 E 206 | 47 L 207 | 48 A 208 | 49 P 209 | 50 L 210 | 51 G 211 | 52 S 212 | 53 L 213 | 54 L 214 | 55 D 215 | 56 R 216 | 57 L 217 | 58 R 218 | 59 K 219 | 60 Y 242 |
■ | ■ | ■ | ■ | ■▲▲ | ■ | ■ | |||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 L 243 | 62 E 244 | 63 S 245 | 64 K 246 | 65 R 247 | 66 F 248 | 67 I 249 | 68 H 250 | 69 R 251 | 70 D 252 | 71 L 253 | 72 A 254 | 73 A 255 | 74 R 256 | 75 N 257 | 76 L 258 | 77 L 259 | 78 L 260 | 79 I 268 | 80 G 269 |
■ | ■♦ | ■ | ■ | ■ | ■ | ||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 270 | 82 F 271 | 83 _ _ | 84 _ _ | 85 _ _ | |||||||||||||||
■▲ | ■ |
Binding affinities
ChEMBL ID:CHEMBL4214342Bioaffinities: 2 records for 2 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 2 | 9 | 9 | 9 | pIC50 | 1 |
Homo sapiens | Tyrosine kinase non-receptor protein 2 | 8.1 | 8.1 | 8.1 | pIC50 | 1 |