6FEK - chain A (model A) | Ret proto-oncogene
Structure information
PDB:6FEK
PubMed:29434222
Release date:2018-02-28
Resolution:2.3 Å
 
Kinase:RET
Family:Ret
Group:TK
Species:HUMAN
 
Quality Score:8
Missing Residues:0
Missing Atoms:31
DFG conformation:in
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:No
 
 
ASP rotation (xDFG.81) :305°
PHE rotation (xDFG.82) :15°
Activation loop position:-3.2Å
αC-helix position:16.7Å
 
G-rich loop angle:51.4°
G-rich loop distance:15.3Å
G-rich loop rotation:58.4°
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
No waters were found in the defined clusters
Binding pocket sequence
UniprotKTLGEGEFGKVVKVAVKMLDLLSEFNVLKQVNPHVIKLYGALLIVEYAKYGSLRGFLREYLAEMKLVHRDLAARNILVISDFGLS
Structure:KTLGEGEFGKVVKVAVKMLDLLSEFNVLKQVNPHVIKLYGALLIVEYAKYGSLRGFLREYLAEMKLVHRDLAARNILVISDFGLS


Modified residues
Residue 900 (not in pocket)
Phosphorylated tyrosine
Residue 905 (not in pocket)
Phosphorylated tyrosine
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: ADN
Ligand Name: ADENOSINE

  • 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
728
2 T
729
3 L
730
4 G
731
5 E
732
6 G
733
7 E
734
8 F
735
9 G
736
10 K
737
11 V
738
12 V
739
13 K
740
14 V
755
15 A
756
16 V
757
17 K
758
18 M
759
19 L
760
20 D
771
αC b.l IV
21 L
772
22 L
773
23 S
774
24 E
775
25 F
776
26 N
777
27 V
778
28 L
779
29 K
780
30 Q
781
31 V
782
32 N
783
33 P
785
34 H
786
35 V
787
36 I
788
37 K
789
38 L
790
39 Y
791
40 G
792
IV V GK hinge linker αD αE
41 A
793
42 L
801
43 L
802
44 I
803
45 V
804
46 E
805
47 Y
806
48 A
807
49 K
808
50 Y
809
51 G
810
52 S
811
53 L
812
54 R
813
55 G
814
56 F
815
57 L
816
58 R
817
59 E
818
60 Y
864
αE VI c.l VII VIII x
61 L
865
62 A
866
63 E
867
64 M
868
65 K
869
66 L
870
67 V
871
68 H
872
69 R
873
70 D
874
71 L
875
72 A
876
73 A
877
74 R
878
75 N
879
76 I
880
77 L
881
78 V
882
79 I
890
80 S
891
DFG a.l
81 D
892
82 F
893
83 G
894
84 L
895
85 S
896

Interaction pattern search
Search KLIFS for kinase-ligand complexes with similar interaction patterns:
Specify the minimum similarity (0.00 no similarity, 1.00 identical)
Binding affinities
ChEMBL ID:CHEMBL477
Bioaffinities: 2 records for 1 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensMitogen-activated protein kinase kinase kinase 74.54.55.4pKd2