4YJV - chain A (model C) | Spleen tyrosine kinase
Structure information
PDB:4YJV
PubMed:21903390
Release date:2015-10-14
Resolution:1.65 Å
 
Kinase:SYK
Family:Syk
Group:TK
Species:HUMAN
 
Quality Score:7.2
Missing Residues:6
Missing Atoms:4
DFG conformation:in
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:No (5Å)
 
 
ASP rotation (xDFG.81) :345°
PHE rotation (xDFG.82) :17°
Activation loop position:-3.6Å
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

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I3
No H-bonds
I4
H-bond protein
I5
H-bond protein
Binding pocket sequence
UniprotKELGSGNFGTVKKVAVKILELLAEANVMQQLDPYIVRMIGIMLVMEMAELGPLNKYLQQYLEESNFVHRDLAARNVLLISDFGLS
Structure:KELG_____TVKKVAVKILELLAEANVMQQLDPYIVRMIGIMLVMEMAELGPLNKYLQQYLEESNFVHRDLAA_NVLLISDFGLS


Modified residues
Residue 525 (not in pocket)
Phosphorylated tyrosine
Residue 526 (not in pocket)
Phosphorylated tyrosine
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: 4DT
Ligand Name: 3-[6-({4-[ethyl(1H-indazol-4-yl)amino]-5-fluoropyrimidin-2-yl}amino)-2,4-dihydro-1H-indazol-1-yl]propan-1-ol

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  • KLIFS residue #
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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
375
2 E
376
3 L
377
4 G
383
5 _
_
6 _
_
7 _
_
8 _
_
9 _
_
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 _
_
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

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Binding affinities
Ligand not found in ChEMBL.