KLIFS - the kinase structures database

Version: 3.2
Updated: 29-Oct-2025

Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform

Kinase structure
Kinase:	Pik3cd (p110d)
Family:	PIK
Group:	Atypical
Species:	MOUSE
PDB:	2WXP
sc-PDB:
KIDFamMap:	Search
Release date:	2010-01-12
PubMed:	20081827
Chain:	A
Orthosteric ligand:	GD9

Structural information
DFG conformation:	in
αC-helix conformation:	in
G-rich loop angle (distance):	62.3° (18.9Å)
G-rich loop rotation:	83°
Quality Score:	7.6
Resolution:	2.3 Å
Missing Residues:	0
Missing Atoms:	0

Ligand binding mode
Pockets	Subpockets
front gate	BP-I-B

Pocket alignment
Uniprot sequence:	CTFMDSKMKPLWIIIFKNGDLRQDMLTLQMIQLRMTPYGCLTGLIEVVLSDTIANIQLNATYV--LGIGDRHSDNIMIHIDFGHF
Sequence structure:	CTFMDSKMKPLWIIIFKNGDLRQDMLTLQMIQLRMTPYGCLTGLIEVVLSDTIANIQLNATYV__LGIGDRHSDNIMIHIDFGHF

Ligand affinity
ChEMBL ID:	CHEMBL521851
Bioaffinities:	67 records for 43 kinases

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Adaptor-associated kinase	5	5	5	pKd	1
Homo sapiens	CaM kinase I alpha	5.3	5.3	5.3	pKd	1
Homo sapiens	CaM kinase I gamma	5.2	5.2	5.2	pKd	1
Homo sapiens	Casein kinase I delta	5.9	5.9	5.9	pKd	1
Homo sapiens	Casein kinase I epsilon	5.9	5.9	5.9	pKd	1
Homo sapiens	Casein kinase II alpha (prime)	5.6	5.6	5.6	pKd	1
Homo sapiens	c-Jun N-terminal kinase 1	5.8	5.8	5.8	pKd	1
Homo sapiens	c-Jun N-terminal kinase 1	5.8	5.8	5.8	pKi	1
Homo sapiens	c-Jun N-terminal kinase 2	5.8	5.8	5.8	pKd	1
Homo sapiens	c-Jun N-terminal kinase 3	6.3	6.3	6.3	pKd	1
Homo sapiens	Cyclin-dependent kinase 7	5.4	5.4	5.4	pKi	1
Homo sapiens	Death-associated protein kinase 1	5.4	5.4	5.4	pKd	1
Homo sapiens	Death-associated protein kinase 3	5.8	5.8	5.8	pKd	1
Homo sapiens	DNA-dependent protein kinase	5.9	5.9	5.9	pIC50	1
Homo sapiens	DNA-dependent protein kinase	5.9	5.9	5.9	pKd	1
Homo sapiens	Dual specificity protein kinase CLK2	6.2	6.2	6.2	pKd	1
Homo sapiens	Dual specificity protein kinase CLK4	5.8	5.8	5.8	pKd	1
Homo sapiens	Dual specificity protein kinase CLK4	6	6	6	pKi	1
Homo sapiens	Dual specificity protein kinase TTK	5.4	5.4	5.4	pKd	1
Homo sapiens	Dual specificity tyrosine-phosphorylation-regulated kinase 1B	5.4	5.4	5.4	pKd	1
Homo sapiens	Dual-specificity tyrosine-phosphorylation regulated kinase 2	5.1	5.1	5.1	pKd	1
Homo sapiens	Dual specificty protein kinase CLK1	6	6	6	pKd	1
Homo sapiens	Homeodomain-interacting protein kinase 1	6	6	6	pKd	1
Homo sapiens	Homeodomain-interacting protein kinase 2	6.3	6.3	6.3	pKd	1
Homo sapiens	Homeodomain-interacting protein kinase 3	6.2	6.2	6.2	pKd	1
Homo sapiens	Homeodomain-interacting protein kinase 4	5.3	5.3	5.3	pKd	1
Homo sapiens	Interleukin-1 receptor-associated kinase 3	5.8	5.8	5.8	pKd	1
Homo sapiens	Leucine-rich repeat serine/threonine-protein kinase 2	5.6	5.6	5.6	pKi	1
Homo sapiens	Maternal embryonic leucine zipper kinase	5.2	5.2	5.2	pKd	1
Homo sapiens	Myosin light chain kinase family member 4	6.1	6.1	6.1	pKd	1
Homo sapiens	Nerve growth factor receptor Trk-A	5.5	5.5	5.5	pIC50	1
Homo sapiens	Ribosomal protein S6 kinase alpha 3	5.5	5.5	5.5	pKd	2
Homo sapiens	Ribosomal protein S6 kinase alpha 6	5.3	5.3	5.3	pKd	2
Homo sapiens	Serine/threonine-protein kinase 16	6	6	6	pKd	1
Homo sapiens	Serine/threonine-protein kinase AKT	7.4	7.3	7.6	pIC50	3
Homo sapiens	Serine/threonine-protein kinase GAK	5.6	5.6	5.6	pKd	1
Homo sapiens	Serine/threonine-protein kinase ICK	5	5	5	pKd	1
Homo sapiens	Serine/threonine-protein kinase mTOR	6.4	6.2	6.9	pIC50	6
Homo sapiens	Serine/threonine-protein kinase mTOR	6.7	6.7	7.3	pKd	2
Homo sapiens	Serine/threonine-protein kinase mTOR	6.2	6.2	6.2	pKi	3
Homo sapiens	Serine/threonine-protein kinase PCTAIRE-1	6	6	6	pKd	1
Homo sapiens	Serine/threonine-protein kinase PCTAIRE-3	5.3	5.3	5.3	pKd	1
Homo sapiens	Serine/threonine-protein kinase PLK4	5.6	5.6	5.6	pKd	1
Homo sapiens	Serine/threonine-protein kinase RIO2	6.2	6.2	6.2	pKd	1
Homo sapiens	SPS1/STE20-related protein kinase YSK4	5.4	5.4	5.4	pKd	1
Homo sapiens	Tyrosine-protein kinase JAK1	6.4	6.4	6.4	pKd	2
Homo sapiens	Tyrosine-protein kinase receptor FLT3	5.6	5.4	6.2	pKd	6
Homo sapiens	Tyrosine-protein kinase TYK2	5.8	5.8	5.8	pKd	2

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 C
749

2 T
750

3 F
751

4 M
752

5 D
753

6 S
754

7 K
755

8 M
756

9 K
757

10 P
758

11 L
759

12 W
760

13 I
761

14 I
776

15 I
777

16 F
778

17 K
779

18 N
780

19 G
781

20 D
783

•

••

•

αC

b.l

21 L
784

22 R
785

23 Q
786

24 D
787

25 M
788

26 L
789

27 T
790

28 L
791

29 Q
792

30 M
793

31 I
794

32 Q
795

33 L
808

34 R
809

35 M
810

36 T
811

37 P
812

38 Y
813

39 G
814

40 C
815

•

•••

hinge

linker

αD

αE

41 L
816

42 T
822

43 G
823

44 L
824

45 I
825

46 E
826

47 V
827

48 V
828

49 L
829

50 S
831

51 D
832

52 T
833

53 I
834

54 A
835

55 N
836

56 I
837

57 Q
838

58 L
839

59 N
840

60 A
885

•

••

•

αE

c.l

VII

VIII

61 T
886

62 Y
887

63 V
888

64 _
_

65 _
_

66 L
889

67 G
890

68 I
891

69 G
892

70 D
893

71 R
894

72 H
895

73 S
896

74 D
897

75 N
898

76 I
899

77 M
900

78 I
901

79 H
909

80 I
910

•

DFG

a.l

81 D
911

82 F
912

83 G
913

84 H
914

85 F
915

••

Interaction pattern search

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