5LMB - chain B (model B) | Spleen tyrosine kinase
Structure information
PDB: | 5LMB |
PubMed: | 27578246 |
Release date: | 2016-09-14 |
Resolution: | 1.95 Å |
Kinase: | SYK |
Family: | Syk |
Group: | TK |
Species: | HUMAN |
Quality Score: | 8 |
Missing Residues: | 0 |
Missing Atoms: | 0 |
DFG conformation: | in |
αC-helix conformation: | in |
Salt bridge KIII.17 and EαC.24: | Yes (2.6Å) |
ASP rotation (xDFG.81) : | 352° |
PHE rotation (xDFG.82) : | 14° |
Activation loop position: | -3.5Å |
αC-helix position: | 17.9Å |
G-rich loop angle: | 56.9° |
G-rich loop distance: | 17.6Å |
G-rich loop rotation: | 74° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I4
H-bond protein
I5
H-bond protein
I10
H-bond protein
I11
H-bond ligand
H-bond protein
Binding pocket sequence
Uniprot | KELGSGNFGTVKKVAVKILELLAEANVMQQLDPYIVRMIGIMLVMEMAELGPLNKYLQQYLEESNFVHRDLAARNVLLISDFGLS |
Structure: | KELGSGNFGTVKKVAVKILELLAEANVMQQLDPYIVRMIGIMLVMEMAELGPLNKYLQQYLEESNFVHRDLAARNVLLISDFGLS |
Modified residues
Residue 525 (not in pocket)
Phosphorylated tyrosine
Orthosteric ligand
Ligand HET-code: 6ZF
Ligand Name: 7-[6-(dimethylamino)pyridin-3-yl]-~{n}-[[(3~{s})-piperidin-3-yl]methyl]pyrido[3,4-b]pyrazin-5-amine
- Download image
- 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 K 375 | 2 E 376 | 3 L 377 | 4 G 378 | 5 S 379 | 6 G 380 | 7 N 381 | 8 F 382 | 9 G 383 | 10 T 384 | 11 V 385 | 12 K 386 | 13 K 387 | 14 V 399 | 15 A 400 | 16 V 401 | 17 K 402 | 18 I 403 | 19 L 404 | 20 E 416 |
■ | ■ | ■ | ■ | ||||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 L 417 | 22 L 418 | 23 A 419 | 24 E 420 | 25 A 421 | 26 N 422 | 27 V 423 | 28 M 424 | 29 Q 425 | 30 Q 426 | 31 L 427 | 32 D 428 | 33 P 430 | 34 Y 431 | 35 I 432 | 36 V 433 | 37 R 434 | 38 M 435 | 39 I 436 | 40 G 437 |
■ | |||||||||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 I 438 | 42 M 445 | 43 L 446 | 44 V 447 | 45 M 448 | 46 E 449 | 47 M 450 | 48 A 451 | 49 E 452 | 50 L 453 | 51 G 454 | 52 P 455 | 53 L 456 | 54 N 457 | 55 K 458 | 56 Y 459 | 57 L 460 | 58 Q 461 | 59 Q 462 | 60 Y 484 |
■ | ■ | ■ | ■▲ | ■ | ■ | ■ | ■ | ■ | |||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 L 485 | 62 E 486 | 63 E 487 | 64 S 488 | 65 N 489 | 66 F 490 | 67 V 491 | 68 H 492 | 69 R 493 | 70 D 494 | 71 L 495 | 72 A 496 | 73 A 497 | 74 R 498 | 75 N 499 | 76 V 500 | 77 L 501 | 78 L 502 | 79 I 510 | 80 S 511 |
■▲ | ■ | ■ | |||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 512 | 82 F 513 | 83 G 514 | 84 L 515 | 85 S 516 | |||||||||||||||
■▲● |
Binding affinities
ChEMBL ID:CHEMBL4528289Bioaffinities: 3 records for 2 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Serine/threonine-protein kinase Aurora-B | 6.6 | 6.6 | 6.6 | pIC50 | 1 |
Homo sapiens | Tyrosine-protein kinase SYK | 6.5 | 6.5 | 7.8 | pIC50 | 2 |