4DG3 - chain E | Protein kinase, cAMP dependent, catalytic, alpha
Structure information
PDB:4DG3
PubMed:-
Release date:2013-02-13
Resolution:1.8 Å
 
Kinase:Prkaca (PKACa)
Family:PKA
Group:AGC
Species:MOUSE
 
Quality Score:9.3
Missing Residues:0
Missing Atoms:7
DFG conformation:in
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes (2.7Å)
 
 
ASP rotation (xDFG.81) :336°
PHE rotation (xDFG.82) :
Activation loop position:-4.2Å
αC-helix position:17.4Å
 
G-rich loop angle:49.4°
G-rich loop distance:15.3Å
G-rich loop rotation:49°
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond protein
I4
H-bond protein
I5
H-bond ligand
H-bond protein
I11
H-bond ligand
H-bond protein
Binding pocket sequence
UniprotKTLGTGSFGRVMLYAMKILHTLNEKRILQAVNPFLVKLEFSYMVMEYVAGGEMFSHLRRYLHSLDLIYRDLKPENLLIVTDFGFA
Structure:KTLGTGSFGRVMLYAMKILHTLNEKRILQAVNPFLVKLEFSYMVMEYVAGGEMFSHLRRYLHSLDLIYRDLKPENLLIVTDFGFA


Modified residues
Residue 139 (not in pocket)
Phosphorylated serine
Residue 197 (not in pocket)
Phosphorylated threonine
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 #
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  • COLORS
  • Interaction types
  • KLIFS (all res.)
  • KLIFS (interacting res.)
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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 K
47
2 T
48
3 L
49
4 G
50
5 T
51
6 G
52
7 S
53
8 F
54
9 G
55
10 R
56
11 V
57
12 M
58
13 L
59
14 Y
69
15 A
70
16 M
71
17 K
72
18 I
73
19 L
74
20 H
87
αC b.l IV
21 T
88
22 L
89
23 N
90
24 E
91
25 K
92
26 R
93
27 I
94
28 L
95
29 Q
96
30 A
97
31 V
98
32 N
99
33 P
101
34 F
102
35 L
103
36 V
104
37 K
105
38 L
106
39 E
107
40 F
108
IV V GK hinge linker αD αE
41 S
109
42 Y
117
43 M
118
44 V
119
45 M
120
46 E
121
47 Y
122
48 V
123
49 A
124
50 G
125
51 G
126
52 E
127
53 M
128
54 F
129
55 S
130
56 H
131
57 L
132
58 R
133
59 R
134
60 Y
156
αE VI c.l VII VIII x
61 L
157
62 H
158
63 S
159
64 L
160
65 D
161
66 L
162
67 I
163
68 Y
164
69 R
165
70 D
166
71 L
167
72 K
168
73 P
169
74 E
170
75 N
171
76 L
172
77 L
173
78 I
174
79 V
182
80 T
183
DFG a.l
81 D
184
82 F
185
83 G
186
84 F
187
85 A
188

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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).