6YID - chain D (model A) | Unc-51 like autophagy activating kinase 2
Structure information
PDB:6YID
PubMed:33200929
Release date:2020-06-17
Resolution:2.7 Å
 
Kinase:ULK2
Family:ULK
Group:Other
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:No (5.2Å)
 
 
ASP rotation (xDFG.81) :344°
PHE rotation (xDFG.82) :12°
Activation loop position:-3.7Å
αC-helix position:17.5Å
 
G-rich loop angle:59.6°
G-rich loop distance:17.1Å
G-rich loop rotation:53.9°
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
UniprotDLVGHGAFAVVFRVAIKSILLGKEIKILKELQENIVALYDVFLVMEYCNGGDLADYLQAILHSKGIIHRDLKPQNILLIADFGFA
Structure:DLVGHGAFAVVFRVAIKSILLGKEIKILKELQENIVALYDVFLVMEYCNGGDLADYLQAILHSKGIIHRDLKPQNILLIADFGFA


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: EDJ
Ligand Name: 2-({5-bromo-2-[(3,4,5-trimethoxyphenyl)amino]pyrimidin-4-yl}oxy)-N-methylbenzene-1-carboximidic acid

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  • LABELS
  • KLIFS residue #
  • Amino Acid
  • None
  • COLORS
  • Interaction types
  • KLIFS (all res.)
  • KLIFS (interacting res.)
  • None
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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 D
13
2 L
14
3 V
15
4 G
16
5 H
17
6 G
18
7 A
19
8 F
20
9 A
21
10 V
22
11 V
23
12 F
24
13 R
25
14 V
36
15 A
37
16 I
38
17 K
39
18 S
40
19 I
41
20 L
52
αC b.l IV
21 L
53
22 G
54
23 K
55
24 E
56
25 I
57
26 K
58
27 I
59
28 L
60
29 K
61
30 E
62
31 L
63
32 Q
64
33 E
66
34 N
67
35 I
68
36 V
69
37 A
70
38 L
71
39 Y
72
40 D
73
IV V GK hinge linker αD αE
41 V
74
42 F
82
43 L
83
44 V
84
45 M
85
46 E
86
47 Y
87
48 C
88
49 N
89
50 G
90
51 G
91
52 D
92
53 L
93
54 A
94
55 D
95
56 Y
96
57 L
97
58 Q
98
59 A
99
60 I
121
αE VI c.l VII VIII x
61 L
122
62 H
123
63 S
124
64 K
125
65 G
126
66 I
127
67 I
128
68 H
129
69 R
130
70 D
131
71 L
132
72 K
133
73 P
134
74 Q
135
75 N
136
76 I
137
77 L
138
78 L
139
79 I
156
80 A
157
DFG a.l
81 D
158
82 F
159
83 G
160
84 F
161
85 A
162

Interaction pattern search
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Binding affinities
ChEMBL ID:CHEMBL4128069
Bioaffinities: 4 records for 2 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensSerine/threonine-protein kinase ULK1777pIC502
Homo sapiensSerine/threonine-protein kinase ULK26.26.28pIC502