5L4Q - chain A (model A) | AP2 associated kinase 1
Structure information
PDB:5L4Q
PubMed:31136173
Release date:2016-06-08
Resolution:1.97 Å
 
Kinase:AAK1
Family:NAK
Group:Other
Species:HUMAN
 
Quality Score:9.7
Missing Residues:0
Missing Atoms:3
DFG conformation:in
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes
 
 
ASP rotation (xDFG.81) :340°
PHE rotation (xDFG.82) :10°
Activation loop position:-3.7Å
αC-helix position:18.2Å
 
G-rich loop angle:52.7°
G-rich loop distance:16Å
G-rich loop rotation:35.3°
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I3
H-bond protein
I4
H-bond protein
I5
H-bond ligand
H-bond protein
Binding pocket sequence
UniprotEVLAEGGFAIVFLCALKRMVCKREIQIMRDLSKNIVGYIDSLILMDFCRGGQVVNLMNQHQCKTPIIHRDLKVENILLLCDFGSA
Structure:EVLAEGGFAIVFLCALKRMVCKREIQIMRDLSKNIVGYIDSLILMDFCRGGQVVNLMNQHQCKTPIIHRDLKVENILLLCDFGSA


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: LKB
Ligand Name: ~{N}-[5-(4-cyanophenyl)-1~{H}-pyrrolo[2,3-b]pyridin-3-yl]pyridine-3-carboxamide

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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
Kinase-ligand interaction pattern
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
50
2 V
51
3 L
52
4 A
53
5 E
54
6 G
55
7 G
56
8 F
57
9 A
58
10 I
59
11 V
60
12 F
61
13 L
62
14 C
71
15 A
72
16 L
73
17 K
74
18 R
75
19 M
76
20 V
86
αC b.l IV
21 C
87
22 K
88
23 R
89
24 E
90
25 I
91
26 Q
92
27 I
93
28 M
94
29 R
95
30 D
96
31 L
97
32 S
98
33 K
101
34 N
102
35 I
103
36 V
104
37 G
105
38 Y
106
39 I
107
40 D
108
IV V GK hinge linker αD αE
41 S
109
42 L
123
43 I
124
44 L
125
45 M
126
46 D
127
47 F
128
48 C
129
49 R
130
50 G
131
51 G
132
52 Q
133
53 V
134
54 V
135
55 N
136
56 L
137
57 M
138
58 N
139
59 Q
140
60 H
166
αE VI c.l VII VIII x
61 Q
167
62 C
168
63 K
169
64 T
170
65 P
171
66 I
172
67 I
173
68 H
174
69 R
175
70 D
176
71 L
177
72 K
178
73 V
179
74 E
180
75 N
181
76 I
182
77 L
183
78 L
184
79 L
192
80 C
193
DFG a.l
81 D
194
82 F
195
83 G
196
84 S
197
85 A
198

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Binding affinities
ChEMBL ID:CHEMBL516312
Bioaffinities: 19 records for 10 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensAdaptor-associated kinase5.95.95.9pIC501
Homo sapiensAdaptor-associated kinase7.36.97.3pKd3
Homo sapiensAdaptor-associated kinase6.36.36.3pKi1
Homo sapiensBMP-2-inducible protein kinase555pIC501
Homo sapiensBMP-2-inducible protein kinase5.45.45.4pKi1
Homo sapiensSerine/threonine-protein kinase 116.46.46.4pKd2
Homo sapiensSerine/threonine-protein kinase 164.74.74.7pIC501
Homo sapiensSerine/threonine-protein kinase 167.67.67.6pKd1
Homo sapiensSerine/threonine-protein kinase 164.94.94.9pKi1
Homo sapiensSerine/threonine-protein kinase GAK5.55.55.5pIC501
Homo sapiensSerine/threonine-protein kinase GAK5.85.85.8pKi1
Homo sapiensSerine/threonine-protein kinase MST27.17.17.1pKd1
Homo sapiensSerine/threonine-protein kinase NEK26.36.36.3pKd1
Homo sapiensSerine/threonine-protein kinase PIM17.57.57.5pKd1
Homo sapiensTRAF2- and NCK-interacting kinase6.86.86.8pKd1
Homo sapiensTyrosine-protein kinase receptor UFO6.26.26.2pKd1