5DBX - chain A (model A) | Serine/threonine kinase 39
Structure information
PDB:5DBX
PubMed:26208601
Release date:2015-09-23
Resolution:2.5 Å
 
Kinase:Stk39 (STLK3)
Family:STE20
Group:STE
Species:MOUSE
 
Quality Score:7.6
Missing Residues:1
Missing Atoms:0
DFG conformation:in
αC-helix conformation:out
Salt bridge KIII.17 and EαC.24:No (17.4Å)
 
 
ASP rotation (xDFG.81) :°
PHE rotation (xDFG.82) :180°
Activation loop position:-4.4Å
αC-helix position:24.5Å
 
G-rich loop angle:56.7°
G-rich loop distance:16.8Å
G-rich loop rotation:42.8°
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
UniprotEVIGSGATAVVQAVAIKRIELLKEIQAMSQCSPNVVTYYTSWLVMKLLSGGSMLDIIKYYLHRNGQIHRDLKAGNILLIADFGVS
Structure:EVIGSGATAVVQAVAIKRIELLKEIQAMSQ_SPNVVTYYTSWLVMKLLSGGSMLDIIKYYLHRNGQIHRDLKAGNILLIADFGVS


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: ANP
Ligand Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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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 E
79
2 V
80
3 I
81
4 G
82
5 S
83
6 G
84
7 A
85
8 T
86
9 A
87
10 V
88
11 V
89
12 Q
90
13 A
91
14 V
101
15 A
102
16 I
103
17 K
104
18 R
105
19 I
106
20 E
117
αC b.l IV
21 L
118
22 L
119
23 K
120
24 E
121
25 I
122
26 Q
123
27 A
124
28 M
125
29 S
126
30 Q
127
31 _
_
32 S
129
33 P
131
34 N
132
35 V
133
36 V
134
37 T
135
38 Y
136
39 Y
137
40 T
138
IV V GK hinge linker αD αE
41 S
139
42 W
147
43 L
148
44 V
149
45 M
150
46 K
151
47 L
152
48 L
153
49 S
154
50 G
155
51 G
156
52 S
157
53 M
158
54 L
159
55 D
160
56 I
161
57 I
162
58 K
163
59 Y
164
60 Y
194
αE VI c.l VII VIII x
61 L
195
62 H
196
63 R
197
64 N
198
65 G
199
66 Q
200
67 I
201
68 H
202
69 R
203
70 D
204
71 L
205
72 K
206
73 A
207
74 G
208
75 N
209
76 I
210
77 L
211
78 L
212
79 I
220
80 A
221
DFG a.l
81 D
222
82 F
223
83 G
224
84 V
225
85 S
226

Interaction pattern search
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Binding affinities
ChEMBL ID:CHEMBL1230989

Bioaffinities: No (p)Ki/(p)IC50/(p)EC50 values for kinases found (with a ChEMBL confidence ≥ 8).