4YFI - chain A (model B) | TNNI3 interacting kinase
Structure information
PDB:4YFI
PubMed:26355916
Release date:2015-09-23
Resolution:2.7 Å
 
Kinase:TNNI3K (HH498)
Family:MLK
Group:TKL
Species:HUMAN
 
Quality Score:9.9
Missing Residues:0
Missing Atoms:1
DFG conformation:in
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes (3Å)
 
 
ASP rotation (xDFG.81) :358°
PHE rotation (xDFG.82) :20°
Activation loop position:-3.4Å
αC-helix position:19.1Å
 
G-rich loop angle:53.1°
G-rich loop distance:16.2Å
G-rich loop rotation:64.3°
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond protein
I2
H-bond protein
I4
H-bond ligand
H-bond protein
Binding pocket sequence
UniprotEIIGSGSFGKVYKVAIKRYMFCREVSILCQLNPCVIQFVGAAIVTQYISGGSLFSLLHEHNLTQPIIHRDLNSHNILLVADFGES
Structure:EIIGSGSFGKVYKVAIKRYMFCREVSILCQLNPCVIQFVGAAIVTQYISGGSLFSLLHEHNLTQPIIHRDLNSHNILLVADFGES


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: 4CW
Ligand Name: N-methyl-3-(9H-purin-6-ylamino)benzenesulfonamide

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  • LABELS
  • KLIFS residue #
  • Amino Acid
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  • 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
467
2 I
468
3 I
469
4 G
470
5 S
471
6 G
472
7 S
473
8 F
474
9 G
475
10 K
476
11 V
477
12 Y
478
13 K
479
14 V
487
15 A
488
16 I
489
17 K
490
18 R
491
19 Y
492
20 M
505
αC b.l IV
21 F
506
22 C
507
23 R
508
24 E
509
25 V
510
26 S
511
27 I
512
28 L
513
29 C
514
30 Q
515
31 L
516
32 N
517
33 P
519
34 C
520
35 V
521
36 I
522
37 Q
523
38 F
524
39 V
525
40 G
526
IV V GK hinge linker αD αE
41 A
527
42 A
536
43 I
537
44 V
538
45 T
539
46 Q
540
47 Y
541
48 I
542
49 S
543
50 G
544
51 G
545
52 S
546
53 L
547
54 F
548
55 S
549
56 L
550
57 L
551
58 H
552
59 E
553
60 H
578
αE VI c.l VII VIII x
61 N
579
62 L
580
63 T
581
64 Q
582
65 P
583
66 I
584
67 I
585
68 H
586
69 R
587
70 D
588
71 L
589
72 N
590
73 S
591
74 H
592
75 N
593
76 I
594
77 L
595
78 L
596
79 V
604
80 A
605
DFG a.l
81 D
606
82 F
607
83 G
608
84 E
609
85 S
610

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Binding affinities
ChEMBL ID:CHEMBL3612641
Bioaffinities: 4 records for 2 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensSerine/threonine-protein kinase B-raf7.57.57.5pIC501
Homo sapiensSerine/threonine-protein kinase TNNI3K6.36.36.3pIC502
Homo sapiensSerine/threonine-protein kinase TNNI3K777pKd1