KLIFS - the structural kinase database

Structure information


PDB:	5KCV
PubMed:	27305487
Release date:	2016-06-29
Resolution:	2.7 Å

Kinase:	AKT1
Family:	Akt
Group:	AGC
Species:	HUMAN

Quality Score:	4
Missing Residues:	7
Missing Atoms:	37

DFG conformation:	out
αC-helix conformation:	na
Salt bridge K^III.17 and E^αC.24:	NA


ASP rotation (xDFG.81) :	157°
PHE rotation (xDFG.82) :	216°
Activation loop position:	1.8Å
αC-helix position:	0Å

G-rich loop angle:	67.5°
G-rich loop distance:	19.7Å
G-rich loop rotation:	49.2°

2D & 3D views

Binding pocket waters

The following waters were found in the defined clusters:

I3

H-bond protein

I9

No H-bonds

Binding pocket sequence

Uniprot	KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVMEYANGGELFFHLSRLHSEKNVVYRDLKLENLMLITDFGLC
Structure:	KLLGKGTFGKVILYAMKIL_______VLQNSRPFLTALKYSCFVMEYANGGELFFHLSRLHSEKNVVYRDLKLENLMLITDFGLC

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: 6S1
Ligand Name: 3-[3-[4-(1-azanylcyclobutyl)phenyl]-5-phenyl-imidazo[4,5-b]pyridin-2-yl]pyridin-2-amine

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LABELS
KLIFS residue #
Amino Acid
None
COLORS
Interaction types
KLIFS (all res.)
KLIFS (interacting res.)
None
OTHER
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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
154

2 L
155

3 L
156

4 G
157

5 K
158

6 G
159

7 T
160

8 F
161

9 G
162

10 K
163

11 V
164

12 I
165

13 L
166

14 Y
176

15 A
177

16 M
178

17 K
179

18 I
180

19 L
181

20 _
_

αC

b.l

IV

21 _
_

22 _
_

23 _
_

24 _
_

25 _
_

26 _
_

27 V
201

28 L
202

29 Q
203

30 N
204

31 S
205

32 R
206

33 P
208

34 F
209

35 L
210

36 T
211

37 A
212

38 L
213

39 K
214

40 Y
215

■

■▲▲

IV

V

GK

hinge

linker

αD

αE

41 S
216

42 C
224

43 F
225

44 V
226

45 M
227

46 E
228

47 Y
229

48 A
230

49 N
231

50 G
232

51 G
233

52 E
234

53 L
235

54 F
236

55 F
237

56 H
238

57 L
239

58 S
240

59 R
241

60 L
264

■

αE

VI

c.l

VII

VIII

x

61 H
265

62 S
266

63 E
267

64 K
268

65 N
269

66 V
270

67 V
271

68 Y
272

69 R
273

70 D
274

71 L
275

72 K
276

73 L
277

74 E
278

75 N
279

76 L
280

77 M
281

78 L
282

79 I
290

80 T
291

■

■♦▲

■

■▲

■

DFG

a.l

81 D
292

82 F
293

83 G
294

84 L
295

85 C
296

■

Interaction pattern search

Search KLIFS for kinase-ligand complexes with similar interaction patterns:

Binding affinities

ChEMBL ID:CHEMBL4297188

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

5KCV - chain A | V-akt murine thymoma viral oncogene homolog 1