3HMI - chain A (model B) | ABL proto-oncogene 2, non-receptor tyrosine kinase
Structure information
PDB: | 3HMI |
PubMed: | - |
Release date: | 2009-07-07 |
Resolution: | 1.65 Å |
Kinase: | ABL2 |
Family: | Abl |
Group: | TK |
Species: | HUMAN |
Quality Score: | 9.5 |
Missing Residues: | 0 |
Missing Atoms: | 5 |
DFG conformation: | out-like |
αC-helix conformation: | in |
Salt bridge KIII.17 and EαC.24: | Yes (2.5Å) |
ASP rotation (xDFG.81) : | 110° |
PHE rotation (xDFG.82) : | 247° |
Activation loop position: | -1.2Å |
αC-helix position: | 19.2Å |
G-rich loop angle: | 56.7° |
G-rich loop distance: | 16.7Å |
G-rich loop rotation: | 16.1° |
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
I5
H-bond protein
Binding pocket sequence
Uniprot | HKLGGGQYGEVYVVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIVTEYMPYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS |
Structure: | HKLGGGQYGEVYVVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIVTEYMPYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: DKI
Ligand Name: 5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE
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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 H 292 | 2 K 293 | 3 L 294 | 4 G 295 | 5 G 296 | 6 G 297 | 7 Q 298 | 8 Y 299 | 9 G 300 | 10 E 301 | 11 V 302 | 12 Y 303 | 13 V 304 | 14 V 314 | 15 A 315 | 16 V 316 | 17 K 317 | 18 T 318 | 19 L 319 | 20 E 328 |
■ | ■ | ■♦ | ■ | ■ | |||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 F 329 | 22 L 330 | 23 K 331 | 24 E 332 | 25 A 333 | 26 A 334 | 27 V 335 | 28 M 336 | 29 K 337 | 30 E 338 | 31 I 339 | 32 K 340 | 33 P 342 | 34 N 343 | 35 L 344 | 36 V 345 | 37 Q 346 | 38 L 347 | 39 L 348 | 40 G 349 |
■ | |||||||||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 V 350 | 42 Y 358 | 43 I 359 | 44 V 360 | 45 T 361 | 46 E 362 | 47 Y 363 | 48 M 364 | 49 P 365 | 50 Y 366 | 51 G 367 | 52 N 368 | 53 L 369 | 54 L 370 | 55 D 371 | 56 Y 372 | 57 L 373 | 58 R 374 | 59 E 375 | 60 Y 399 |
▲ | ■♦ | ■▲▲ | ■ | ||||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 L 400 | 62 E 401 | 63 K 402 | 64 K 403 | 65 N 404 | 66 F 405 | 67 I 406 | 68 H 407 | 69 R 408 | 70 D 409 | 71 L 410 | 72 A 411 | 73 A 412 | 74 R 413 | 75 N 414 | 76 C 415 | 77 L 416 | 78 V 417 | 79 V 425 | 80 A 426 |
■ | ■ | ■ | ■ | ||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 427 | 82 F 428 | 83 G 429 | 84 L 430 | 85 S 431 | |||||||||||||||
■♦ |
Binding affinities
ChEMBL ID:CHEMBL261720Bioaffinities: 7 records for 5 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Dual specificity protein kinase CLK3 | 7.5 | 7.5 | 7.5 | pIC50 | 1 |
Homo sapiens | Dual specificty protein kinase CLK1 | 8.1 | 8.1 | 8.1 | pIC50 | 1 |
Homo sapiens | Glycogen synthase kinase-3 beta | 6.7 | 6.7 | 6.9 | pIC50 | 2 |
Homo sapiens | Interferon-induced, double-stranded RNA-activated protein kinase | 5.8 | 5.8 | 5.8 | pIC50 | 1 |
Homo sapiens | Vascular endothelial growth factor receptor 2 | 7.5 | 7.5 | 7.5 | pIC50 | 2 |