KLIFS - the structural kinase database

Structure information


PDB:	3D0E
PubMed:	18800763
Release date:	2008-10-21
Resolution:	2 Å

Kinase:	AKT2
Family:	Akt
Group:	AGC
Species:	HUMAN

Quality Score:	8
Missing Residues:	0
Missing Atoms:	0

DFG conformation:	in
αC-helix conformation:	in
Salt bridge K^III.17 and E^αC.24:	Yes (2.8Å)


ASP rotation (xDFG.81) :	344°
PHE rotation (xDFG.82) :	0°
Activation loop position:	-4Å
αC-helix position:	18Å

G-rich loop angle:	57.8°
G-rich loop distance:	17.6Å
G-rich loop rotation:	50.3°

Other models from this PDB:

2D & 3D views

Binding pocket waters

The following waters were found in the defined clusters:

I1

H-bond protein

I3

H-bond protein

Binding pocket sequence

Uniprot	KLLGKGTFGKVILYAMKILHTVTESRVLQNTRPFLTALKYACFVMEYANGGELFFHLSRYLHSRDVVYRDIKLENLMLITDFGLC
Structure:	KLLGKGTFGKVILYAMKILHTVTESRVLQNTRPFLTALKYACFVMEYANGGELFFHLSRYLHSRDVVYRDIKLENLMLITDFGLC

Modified residues

Residue 309 (not in pocket)

Phosphorylated threonine

Residue 451 (not in pocket)

Phosphorylated threonine

Orthosteric ligand

Ligand HET-code: G93
Ligand Name: 4-{2-(4-amino-1,2,5-oxadiazol-3-yl)-1-ethyl-7-[(3S)-piperidin-3-ylmethoxy]-1H-imidazo[4,5-c]pyridin-4-yl}-2-methylbut-3-yn-2-ol

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LABELS
KLIFS residue #
Amino Acid
None
COLORS
Interaction types
KLIFS (all res.)
KLIFS (interacting res.)
None
OTHER
Show/hide non-interacting res.
En/disable resizing interacting res.

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
156

2 L
157

3 L
158

4 G
159

5 K
160

6 G
161

7 T
162

8 F
163

9 G
164

10 K
165

11 V
166

12 I
167

13 L
168

14 Y
178

15 A
179

16 M
180

17 K
181

18 I
182

19 L
183

20 H
196

■

αC

b.l

IV

21 T
197

22 V
198

23 T
199

24 E
200

25 S
201

26 R
202

27 V
203

28 L
204

29 Q
205

30 N
206

31 T
207

32 R
208

33 P
210

34 F
211

35 L
212

36 T
213

37 A
214

38 L
215

39 K
216

40 Y
217

■

IV

V

GK

hinge

linker

αD

αE

41 A
218

42 C
226

43 F
227

44 V
228

45 M
229

46 E
230

47 Y
231

48 A
232

49 N
233

50 G
234

51 G
235

52 E
236

53 L
237

54 F
238

55 F
239

56 H
240

57 L
241

58 S
242

59 R
243

60 Y
265

■

▲

♦

■▲

■▲●

αE

VI

c.l

VII

VIII

x

61 L
266

62 H
267

63 S
268

64 R
269

65 D
270

66 V
271

67 V
272

68 Y
273

69 R
274

70 D
275

71 I
276

72 K
277

73 L
278

74 E
279

75 N
280

76 L
281

77 M
282

78 L
283

79 I
291

80 T
292

■▲●

■

DFG

a.l

81 D
293

82 F
294

83 G
295

84 L
296

85 C
297

■▲

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL494089
Bioaffinities: 143 records for 83 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Rattus norvegicus	AMP-activated protein kinase, alpha-2 subunit	7.3	7.3	7.3	pIC50	1
Homo sapiens	AMP-activated protein kinase, gamma-2 subunit	7.1	7.1	7.1	pKd	1
Homo sapiens	CaM kinase I delta	5.6	5.6	5.6	pKd	1
Homo sapiens	CaM kinase IV	6.4	6.4	6.4	pKd	1
Homo sapiens	cAMP-dependent protein kinase alpha-catalytic subunit	7.7	7.7	7.7	pKd	1
Homo sapiens	cAMP-dependent protein kinase beta-1 catalytic subunit	7.4	7.4	7.9	pKd	2
Homo sapiens	cAMP-dependent protein kinase type II-alpha regulatory subunit	7.3	7.3	7.3	pKd	1
Homo sapiens	cGMP-dependent protein kinase 1 beta	7.5	7.5	7.5	pIC50	1
Homo sapiens	cGMP-dependent protein kinase 1 beta	6.7	6.7	7.1	pKd	2
Homo sapiens	cGMP-dependent protein kinase 2	8.5	8.5	8.5	pKd	1
Homo sapiens	Citron Rho-interacting kinase	6.1	6.1	6.7	pKd	2
Homo sapiens	Death-associated protein kinase 1	5.5	5.5	5.5	pKd	1
Homo sapiens	Death-associated protein kinase 3	7.1	7.1	7.1	pIC50	1
Homo sapiens	Death-associated protein kinase 3	6.3	6.3	6.3	pKd	1
Homo sapiens	Dual specificity protein kinase CLK2	6.1	6.1	6.1	pKd	1
Homo sapiens	Ephrin type-A receptor 5	5.4	5.4	5.4	pKd	1
Homo sapiens	Glycogen synthase kinase-3 alpha	5.3	5.3	6.6	pKd	2
Homo sapiens	Glycogen synthase kinase-3 beta	6.9	6.9	6.9	pIC50	1
Homo sapiens	Glycogen synthase kinase-3 beta	6.4	6.4	7	pKd	2
Homo sapiens	G protein-coupled receptor kinase 7	6.4	6.4	6.4	pKd	1
Homo sapiens	Homeodomain-interacting protein kinase 1	6.3	6.3	6.3	pKd	1
Homo sapiens	Homeodomain-interacting protein kinase 2	6.4	6.4	6.4	pKd	1
Homo sapiens	Homeodomain-interacting protein kinase 3	6.7	6.7	6.7	pKd	1
Homo sapiens	Interferon-induced, double-stranded RNA-activated protein kinase	5.7	5.7	5.7	pKd	1
Homo sapiens	MAP/microtubule affinity-regulating kinase 2	6.1	6.1	6.5	pKd	2
Homo sapiens	Maternal embryonic leucine zipper kinase	6.1	6.1	6.1	pKd	1
Homo sapiens	Mitogen-activated protein kinase 15	5.9	5.9	5.9	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 2	6.5	6.5	6.5	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 3	6.1	6.1	6.1	pKd	1
Homo sapiens	NUAK family SNF1-like kinase 1	6.4	6.4	6.4	pKd	1
Homo sapiens	NUAK family SNF1-like kinase 2	7.1	7.1	7.1	pKd	1
Homo sapiens	PAS domain-containing serine/threonine-protein kinase	6	6	6	pKd	1
Homo sapiens	Phosphatidylinositol-4-phosphate 5-kinase type-1 gamma	5.8	5.8	5.8	pKd	1
Homo sapiens	Platelet-derived growth factor receptor beta	5.4	5.4	5.4	pKd	1
Homo sapiens	Protein kinase C alpha	6.3	6.3	6.3	pKd	1
Homo sapiens	Protein kinase C beta	7.7	7.7	7.7	pIC50	1
Homo sapiens	Protein kinase C beta	6.5	6.5	6.5	pKd	1
Homo sapiens	Protein kinase C delta	7.9	7.9	7.9	pIC50	1
Homo sapiens	Protein kinase C delta	7.1	7.1	7.3	pKd	2
Homo sapiens	Protein kinase C epsilon	7.7	7.7	7.7	pIC50	1
Homo sapiens	Protein kinase C epsilon	8.3	8.3	8.3	pKd	1
Homo sapiens	Protein kinase C eta	8.7	8.7	8.7	pIC50	1
Homo sapiens	Protein kinase C eta	8.6	8.6	8.6	pKd	1
Homo sapiens	Protein kinase C iota	5.7	5.7	6.6	pKd	2
Homo sapiens	Protein kinase C mu	5.5	5.5	5.5	pKd	1
Homo sapiens	Protein kinase C nu	6	6	6	pKd	1
Homo sapiens	Protein kinase C theta	8.7	8.7	8.7	pIC50	1
Homo sapiens	Protein kinase C theta	7.8	7.8	8	pKd	2
Homo sapiens	Protein kinase N1	7.4	7.4	7.5	pKd	2
Homo sapiens	Protein kinase N2	5.5	5.5	6.1	pKd	2
Rattus norvegicus	RAC-alpha serine/threonine-protein kinase	5.2	5.2	5.2	pIC50	1
Homo sapiens	Rho-associated protein kinase 1	6.1	6.1	6.1	pIC50	1
Homo sapiens	Rho-associated protein kinase 1	5.6	5.6	6.6	pKd	2
Homo sapiens	Rho-associated protein kinase 2	6	6	6.7	pKd	2
Homo sapiens	Rhodopsin kinase	6.2	6.2	6.2	pKd	1
Homo sapiens	Ribosomal protein S6 kinase alpha 1	5.9	5.9	5.9	pIC50	2
Homo sapiens	Ribosomal protein S6 kinase alpha 4	6.1	6.1	7.3	pKd	4
Homo sapiens	Ribosomal protein S6 kinase alpha 5	5.1	5.1	5.1	pIC50	2
Homo sapiens	Ribosomal protein S6 kinase alpha 5	6.8	6.8	6.8	pKd	2
Homo sapiens	Serine/threonine-protein kinase 36	5.6	5.6	5.6	pKd	1
Homo sapiens	Serine/threonine-protein kinase AKT	8.7	4.8	9.2	pIC50	7
Homo sapiens	Serine/threonine-protein kinase AKT	6.3	6.3	8.7	pKd	2
Homo sapiens	Serine/threonine-protein kinase AKT	9	9	9	pKi	2
Homo sapiens	Serine/threonine-protein kinase AKT2	7.9	7.9	7.9	pIC50	2
Homo sapiens	Serine/threonine-protein kinase AKT2	6.5	6.5	8.7	pKd	2
Homo sapiens	Serine/threonine-protein kinase AKT2	8.4	8.4	8.4	pKi	2
Homo sapiens	Serine/threonine-protein kinase AKT3	8.1	8.1	8.1	pIC50	2
Homo sapiens	Serine/threonine-protein kinase AKT3	5.9	5.9	8.5	pKd	2
Homo sapiens	Serine/threonine-protein kinase AKT3	7.9	7.9	7.9	pKi	1
Homo sapiens	Serine/threonine-protein kinase Chk2	5.3	5.3	5.3	pKd	1
Homo sapiens	Serine/threonine-protein kinase c-TAK1	6.7	6.7	6.7	pKd	1
Homo sapiens	Serine/threonine-protein kinase DCLK1	5.6	5.6	5.6	pKd	1
Homo sapiens	Serine/threonine-protein kinase DCLK3	7	7	7	pKd	1
Homo sapiens	Serine/threonine-protein kinase LATS1	7.1	7.1	7.1	pKd	1
Homo sapiens	Serine/threonine-protein kinase LATS2	6.9	6.9	6.9	pKd	1
Homo sapiens	Serine/threonine-protein kinase MRCK beta	5.8	5.8	5.8	pKd	1
Homo sapiens	Serine/threonine-protein kinase MST4	5.3	5.3	5.3	pKd	1
Homo sapiens	Serine/threonine-protein kinase NEK7	5.7	5.7	5.7	pKd	1
Homo sapiens	Serine/threonine protein kinase NLK	5.5	5.5	5.5	pKd	1
Homo sapiens	Serine/threonine-protein kinase PAK 1	6.3	6.3	6.3	pKd	1
Homo sapiens	Serine/threonine-protein kinase PAK 2	6.6	6.6	6.6	pKd	1
Homo sapiens	Serine/threonine-protein kinase PAK 4	8	8	8	pIC50	1
Homo sapiens	Serine/threonine-protein kinase PAK 4	7.3	7.3	7.8	pKd	2
Homo sapiens	Serine/threonine-protein kinase PAK6	8.2	8.2	8.2	pIC50	1
Homo sapiens	Serine/threonine-protein kinase PAK6	6.8	6.8	7.7	pKd	2
Homo sapiens	Serine/threonine-protein kinase PAK7	7.3	7.3	7.3	pIC50	1
Homo sapiens	Serine/threonine-protein kinase PAK7	8.1	8.1	8.1	pKd	1
Homo sapiens	Serine/threonine-protein kinase PIM1	6	6	6	pKd	1
Homo sapiens	Serine/threonine-protein kinase PIM2	6.2	6.2	6.2	pKd	1
Homo sapiens	Serine/threonine-protein kinase PIM3	6.1	6.1	6.1	pKd	1
Mycobacterium tuberculosis	Serine/threonine-protein kinase pknB	8.5	8.5	8.5	pKd	1
Homo sapiens	Serine/threonine-protein kinase PRKX	8.3	8.3	8.3	pIC50	1
Homo sapiens	Serine/threonine-protein kinase PRKX	8.1	8.1	8.1	pKd	1
Homo sapiens	Serine/threonine-protein kinase Sgk3	5.7	5.7	5.7	pKd	1
Homo sapiens	Serine/threonine-protein kinase SIK2	5.2	5.2	5.2	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO1	6.2	6.2	6.2	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO2	5.9	5.9	5.9	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO3	5	5	5	pKd	1
Homo sapiens	Serine/threonine-protein kinase ULK1	5.2	5.2	5.2	pKd	1
Homo sapiens	Serine/threonine-protein kinase ULK2	5.6	5.6	5.6	pKd	1
Homo sapiens	SPS1/STE20-related protein kinase YSK4	7.5	7.5	7.5	pKd	1
Homo sapiens	Stem cell growth factor receptor	5.8	5.1	6.9	pKd	7
Homo sapiens	Tyrosine-protein kinase receptor RET	5.9	5.9	5.9	pKd	1

3D0E - chain A | V-akt murine thymoma viral oncogene homolog 2