KLIFS - the kinase structures database

Version: 3.2
Updated: 29-Oct-2025

3-phosphoinositide dependent protein kinase 1

Kinase structure
Kinase:	PDPK1 (PDK1)
Family:	PDK1
Group:	AGC
Species:	HUMAN
IUPHAR/BPS ID:	1519
PDB:	1UU3
sc-PDB:
KIDFamMap:	Search
Release date:	2004-03-04
PubMed:	14962382
Chain:	A
(Alternate) Model:	A
Orthosteric ligand:	LY4

More entries for 1UU3
1UU3	Alternative model:	B	Chain:	A

Structural information
DFG conformation:	in
αC-helix conformation:	in
G-rich loop angle (distance):	59.3° (17.3Å)
G-rich loop rotation:	48.6°
Quality Score:	8
Resolution:	1.7 Å
Missing Residues:	0
Missing Atoms:	0

Ligand binding mode
Pockets	Subpockets	Waters
front		Cluster I1 I4	Ligand No No	Protein Yes Yes

Pocket alignment
Uniprot sequence:	KILGEGSFSTVVLYAIKILYVTRERDVMSRLDPFFVKLYFTYFGLSYAKNGELLKYIRKYLHGKGIIHRDLKPENILLITDFGTA
Sequence structure:	KILGEGSFSTVVLYAIKILYVTRERDVMSRLDPFFVKLYFTYFGLSYAKNGELLKYIRKYLHGKGIIHRDLKPENILLITDFGTA

Ligand affinity
ChEMBL ID:	CHEMBL91829
Bioaffinities:	252 records for 117 kinases

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	3-phosphoinositide dependent protein kinase-1	6.1	6.1	6.1	pIC50	1
Homo sapiens	3-phosphoinositide dependent protein kinase-1	6.2	6.2	6.2	pKd	2
Homo sapiens	Adaptor-associated kinase	6.1	6	6.1	pKd	3
Homo sapiens	BMP-2-inducible protein kinase	6.4	5.6	6.4	pKd	3
Homo sapiens	CaM kinase I delta	5.4	5.4	5.6	pKd	2
Homo sapiens	CaM kinase II alpha	5.4	5	5.4	pKd	3
Homo sapiens	CaM kinase II delta	5.3	5.3	5.3	pKd	2
Homo sapiens	CaM kinase II gamma	5.1	5.1	5.1	pKd	2
Homo sapiens	CaM-kinase kinase alpha	5.3	5.3	5.8	pKd	3
Homo sapiens	CaM-kinase kinase beta	5.6	5.6	6	pKd	3
Homo sapiens	cAMP-dependent protein kinase alpha-catalytic subunit	5.3	5.3	5.3	pKd	2
Homo sapiens	cAMP-dependent protein kinase beta-1 catalytic subunit	5.5	5.5	5.5	pKd	2
Homo sapiens	Casein kinase II alpha	5.4	5.4	5.4	pKd	1
Homo sapiens	Casein kinase II alpha (prime)	5.2	5.2	5.5	pKd	2
Homo sapiens	cGMP-dependent protein kinase 2	5.5	5.5	5.5	pKd	2
Homo sapiens	Citron Rho-interacting kinase	5.9	5.9	5.9	pKd	2
Homo sapiens	Cyclin-dependent kinase 4	6.6	6.6	6.6	pKd	2
Homo sapiens	Cyclin-dependent kinase 7	5.8	5.8	5.8	pKd	1
Homo sapiens	Cyclin-dependent kinase-like 5	5.4	5.4	5.4	pKd	1
Homo sapiens	Death-associated protein kinase 1	6	6	6	pKd	2
Homo sapiens	Death-associated protein kinase 2	5.6	5.6	5.6	pKd	1
Homo sapiens	Death-associated protein kinase 3	5.1	5.1	5.9	pKd	2
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 4	6	6	6	pKd	2
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 5	6	6	6	pKd	1
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 6	5.4	5.4	5.4	pKd	1
Homo sapiens	Dual specificity protein kinase CLK2	6.4	6.4	6.4	pKd	2
Homo sapiens	Dual specificity protein kinase CLK4	5.7	5.1	5.7	pKd	3
Homo sapiens	Dual-specificity tyrosine-phosphorylation regulated kinase 1A	6.6	6.6	6.6	pKd	1
Homo sapiens	Dual specificity tyrosine-phosphorylation-regulated kinase 1B	5.3	5.3	5.3	pKd	2
Homo sapiens	Dual specificty protein kinase CLK1	6	6	6	pKd	2
Homo sapiens	Epidermal growth factor receptor erbB1	5.1	5.1	5.3	pKd	2
Homo sapiens	Fibroblast growth factor receptor 1	5.3	5.3	5.3	pKd	1
Homo sapiens	Glycogen synthase kinase-3 beta	5.6	5.6	5.6	pKd	2
Homo sapiens	G protein-coupled receptor kinase 4	6.2	6.2	6.2	pKd	1
Homo sapiens	G protein-coupled receptor kinase 7	6.5	6.5	6.5	pKd	1
Homo sapiens	Homeodomain-interacting protein kinase 1	6.6	6.6	6.6	pKd	1
Homo sapiens	Homeodomain-interacting protein kinase 2	6.9	6.9	6.9	pKd	1
Homo sapiens	Homeodomain-interacting protein kinase 3	7.1	7.1	7.1	pKd	1
Homo sapiens	Leucine-rich repeat serine/threonine-protein kinase 2	5	5	5	pKd	1
Homo sapiens	MAP kinase-interacting serine/threonine-protein kinase MNK1	5.2	5.2	5.2	pKd	1
Homo sapiens	MAP/microtubule affinity-regulating kinase 2	5.6	5.6	5.6	pKd	1
Homo sapiens	Misshapen-like kinase 1	6.5	6.5	6.5	pKd	1
Homo sapiens	Mitogen-activated protein kinase 15	7.1	7.1	7.1	pKd	2
Homo sapiens	Mitogen-activated protein kinase kinase kinase 2	6.2	6.2	6.2	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 3	6.8	6.8	6.8	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 9	5.9	5.9	5.9	pKd	2
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 1	5.6	5.6	5.6	pKd	2
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 2	6.5	6.5	6.5	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 3	5.1	5.1	5.1	pKd	2
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 5	5.1	5.1	5.1	pKd	1
Homo sapiens	Myosin light chain kinase, smooth muscle	6.5	6.5	6.5	pKd	2
Homo sapiens	Myotonin-protein kinase	6.6	6.6	6.6	pKd	2
Homo sapiens	NUAK family SNF1-like kinase 1	5.8	5.8	5.8	pKd	2
Homo sapiens	NUAK family SNF1-like kinase 2	6.5	6.5	6.5	pKd	2
Homo sapiens	Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha	6.2	6.2	6.2	pKd	2
Homo sapiens	Phosphatidylinositol-5-phosphate 4-kinase type-2 beta	6.1	6.1	6.1	pKd	2
Homo sapiens	Phosphorylase kinase gamma subunit 1	5.4	5.4	5.6	pKd	3
Homo sapiens	Platelet-derived growth factor receptor beta	5.2	5.2	5.2	pKd	1
Homo sapiens	Protein kinase C alpha	6.4	6.4	6.4	pIC50	3
Homo sapiens	Protein kinase C beta	8.2	8.2	8.3	pIC50	7
Homo sapiens	Protein kinase C delta	6.6	6.6	6.6	pIC50	1
Homo sapiens	Protein kinase C delta	8.4	8.4	8.4	pKd	2
Homo sapiens	Protein kinase C epsilon	6.2	6.2	6.2	pIC50	2
Homo sapiens	Protein kinase C epsilon	8	8	8	pKd	2
Homo sapiens	Protein kinase C eta	7.3	7.3	7.3	pIC50	1
Homo sapiens	Protein kinase C eta	5.8	5.8	5.8	pKd	2
Homo sapiens	Protein kinase C gamma	6.5	6.5	6.5	pIC50	3
Homo sapiens	Protein kinase C iota	5.9	5.9	5.9	pKd	1
Homo sapiens	Protein kinase C theta	8.6	8.6	8.6	pKd	2
Homo sapiens	Protein kinase N1	6.5	6.5	6.5	pKd	2
Homo sapiens	Protein kinase N2	5.8	5.8	5.8	pKd	2
Homo sapiens	Proto-oncogene tyrosine-protein kinase ROS	5.2	5.2	5.2	pKd	1
Homo sapiens	Rhodopsin kinase	6.1	6.1	6.1	pKd	1
Homo sapiens	Ribosomal protein S6 kinase 1	6.7	6.7	6.7	pKd	1
Homo sapiens	Ribosomal protein S6 kinase alpha 1	6.4	6.4	6.4	pKd	4
Homo sapiens	Ribosomal protein S6 kinase alpha 2	6.6	5.8	6.6	pKd	6
Homo sapiens	Ribosomal protein S6 kinase alpha 3	5.4	5.4	5.7	pKd	6
Homo sapiens	Ribosomal protein S6 kinase alpha 4	5.2	5.2	5.2	pKd	4
Homo sapiens	Ribosomal protein S6 kinase alpha 5	5.9	5.7	5.9	pKd	6
Homo sapiens	Ribosomal protein S6 kinase alpha 6	5.6	5.6	5.6	pKd	4
Homo sapiens	Serine/threonine-protein kinase 10	6.6	6	6.6	pKd	3
Homo sapiens	Serine/threonine-protein kinase 11	5.2	5.2	5.2	pKd	1
Homo sapiens	Serine/threonine-protein kinase 2	6.4	6	6.4	pKd	3
Homo sapiens	Serine/threonine-protein kinase 33	5.5	5.5	5.6	pKd	2
Homo sapiens	Serine/threonine-protein kinase AKT2	5.1	5.1	5.1	pKd	1
Homo sapiens	Serine/threonine-protein kinase AKT3	5.9	5.9	5.9	pKd	2
Homo sapiens	Serine/threonine-protein kinase Aurora-C	5.5	5.5	5.5	pKd	1
Homo sapiens	Serine/threonine-protein kinase Chk1	6.3	6.3	6.3	pKd	2
Homo sapiens	Serine/threonine-protein kinase Chk2	5.4	5.4	5.4	pKd	1
Homo sapiens	Serine/threonine-protein kinase D2	6.1	6.1	6.1	pKd	2
Homo sapiens	Serine/threonine-protein kinase GAK	6	5.9	6	pKd	3
Homo sapiens	Serine/threonine-protein kinase ICK	6.6	6.6	6.6	pKd	1
Homo sapiens	Serine/threonine-protein kinase LATS1	5.6	5.6	5.6	pKd	2
Homo sapiens	Serine/threonine-protein kinase LATS2	6.2	6.2	6.2	pKd	2
Homo sapiens	Serine/threonine-protein kinase MST1	6.7	6.7	6.7	pKd	1
Homo sapiens	Serine/threonine-protein kinase MST2	6	6	6	pKd	2
Mus musculus	Serine/threonine-protein kinase MST2	7.1	7.1	7.1	pKd	1
Homo sapiens	Serine/threonine-protein kinase PCTAIRE-1	5.1	5.1	5.6	pKd	2
Homo sapiens	Serine/threonine-protein kinase PIM1	6.7	6.7	6.7	pIC50	2
Homo sapiens	Serine/threonine-protein kinase PIM1	6.6	6.6	7.3	pKd	4
Homo sapiens	Serine/threonine-protein kinase PIM2	5.8	5.8	6.9	pKd	4
Homo sapiens	Serine/threonine-protein kinase PIM3	7.9	7.9	7.9	pKd	2
Homo sapiens	Serine/threonine-protein kinase PLK4	5.3	5.3	6.4	pKd	3
Homo sapiens	Serine/threonine-protein kinase PRP4 homolog	5.8	5.8	5.8	pKd	1
Homo sapiens	Serine/threonine-protein kinase RIO1	6.1	6.1	6.1	pKd	2
Homo sapiens	Serine/threonine-protein kinase RIO3	6.2	6.2	6.2	pKd	1
Homo sapiens	Serine/threonine-protein kinase Sgk3	5.9	5.9	5.9	pKd	1
Homo sapiens	Serine/threonine-protein kinase SRPK1	5.9	5.9	5.9	pKd	1
Homo sapiens	Serine/threonine-protein kinase SRPK2	6	6	6	pKd	1
Homo sapiens	Serine/threonine-protein kinase SRPK3	5.8	5.8	5.8	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO1	5.8	5.8	5.8	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO2	5.4	5.4	5.4	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO3	7	7	7	pKd	1
Homo sapiens	Serine/threonine-protein kinase TBK1	6	6	6	pKd	1
Homo sapiens	Serine/threonine-protein kinase tousled-like 1	5.7	5.7	5.7	pKd	1
Homo sapiens	SPS1/STE20-related protein kinase YSK4	7.3	7.3	7.3	pKd	1
Homo sapiens	Stem cell growth factor receptor	5.8	5	6.4	pKd	8
Homo sapiens	TRAF2- and NCK-interacting kinase	5.2	5.2	5.2	pKd	1
Homo sapiens	Tyrosine-protein kinase HCK	5.6	5.6	5.6	pKd	1
Homo sapiens	Tyrosine-protein kinase JAK3	5.9	5.9	6.4	pKd	4
Homo sapiens	Tyrosine-protein kinase LCK	5.9	5.9	5.9	pKd	1
Homo sapiens	Tyrosine-protein kinase receptor FLT3	6.6	5.7	6.9	pKd	13

Kinase-ligand interaction pattern

• Hydrophobic • Aromatic face-to-face • Aromatic face-to-edge • H-bond donor • H-bond acceptor • Ionic positive • Ionic negative

g.l

III

αC

1 K
86

2 I
87

3 L
88

4 G
89

5 E
90

6 G
91

7 S
92

8 F
93

9 S
94

10 T
95

11 V
96

12 V
97

13 L
98

14 Y
108

15 A
109

16 I
110

17 K
111

18 I
112

19 L
113

20 Y
126

•

αC

b.l

21 V
127

22 T
128

23 R
129

24 E
130

25 R
131

26 D
132

27 V
133

28 M
134

29 S
135

30 R
136

31 L
137

32 D
138

33 P
140

34 F
141

35 F
142

36 V
143

37 K
144

38 L
145

39 Y
146

40 F
147

•

hinge

linker

αD

αE

41 T
148

42 Y
156

43 F
157

44 G
158

45 L
159

46 S
160

47 Y
161

48 A
162

49 K
163

50 N
164

51 G
165

52 E
166

53 L
167

54 L
168

55 K
169

56 Y
170

57 I
171

58 R
172

59 K
173

60 Y
195

•

••

•

αE

c.l

VII

VIII

61 L
196

62 H
197

63 G
198

64 K
199

65 G
200

66 I
201

67 I
202

68 H
203

69 R
204

70 D
205

71 L
206

72 K
207

73 P
208

74 E
209

75 N
210

76 I
211

77 L
212

78 L
213

79 I
221

80 T
222

•

••

DFG

a.l

81 D
223

82 F
224

83 G
225

84 T
226

85 A
227

•

Interaction pattern search

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