KLIFS - the kinase structures database

Version: 3.2
Updated: 29-Oct-2025

KIT proto-oncogene receptor tyrosine kinase

Kinase structure
Kinase:	KIT
Family:	PDGFR
Group:	TK
Species:	HUMAN
IUPHAR/BPS ID:	1805
PDB:	1T46
sc-PDB:
KIDFamMap:	Search
Release date:	2004-06-15
PubMed:	15123710
Chain:	A
(Alternate) Model:	B
Orthosteric ligand:	STI

More entries for 1T46
1T46	Alternative model:	A	Chain:	A

Structural information
DFG conformation:	out
αC-helix conformation:	in
G-rich loop angle (distance):	57.9° (18.1Å)
G-rich loop rotation:	47.5°
Quality Score:	7.6
Resolution:	1.6 Å
Missing Residues:	0
Missing Atoms:	0

Ligand binding mode
Pockets	Subpockets	Waters
front gate back	BP-I-A BP-I-B BP-II-out BP-IV	Cluster I1 I5 I7	Ligand No Yes No	Protein Yes Yes No

Pocket alignment
Uniprot sequence:	KTLGAGAFGKVVEVAVKMLALMSELKVLSYLGMNIVNLLGALVITEYCCYGDLLNFLRRFLASKNCIHRDLAARNILLICDFGLA
Sequence structure:	KTLGAGAFGKVVEVAVKMLALMSELKVLSYLGMNIVNLLGALVITEYCCYGDLLNFLRRFLASKNCIHRDLAARNILLICDFGLA

Ligand affinity
ChEMBL ID:	CHEMBL941
Bioaffinities:	228 records for 42 kinases

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Cell division cycle 2-like protein kinase 6	5.3	5.3	5.3	pKd	2
Homo sapiens	c-Jun N-terminal kinase 1	5.3	5.3	5.5	pKd	3
Homo sapiens	c-Jun N-terminal kinase 2	5.3	5.3	5.3	pKd	1
Homo sapiens	c-Jun N-terminal kinase 3	5.5	5.5	5.5	pKd	3
Homo sapiens	c-Jun N-terminal kinase 3	6	6	6	pKi	1
Homo sapiens	Discoidin domain-containing receptor 2	6.2	6.2	6.9	pIC50	2
Homo sapiens	Discoidin domain-containing receptor 2	7.8	7.8	7.8	pKd	2
Homo sapiens	Dual specificity protein kinase CLK4	5.7	5.4	5.7	pKd	4
Homo sapiens	Dual specificity protein kinase CLK4	5.9	5.9	5.9	pKi	1
Homo sapiens	Dual specificty protein kinase CLK1	5.4	5.4	5.4	pKd	3
Homo sapiens	Ephrin type-A receptor 8	5.9	5.7	5.9	pKd	3
Homo sapiens	Epidermal growth factor receptor erbB1	5.1	5.1	5.1	pKd	2
Homo sapiens	Epithelial discoidin domain-containing receptor 1	6.5	4.5	7.4	pIC50	4
Homo sapiens	Epithelial discoidin domain-containing receptor 1	9.2	9.2	9.2	pKd	2
Homo sapiens	Homeodomain-interacting protein kinase 4	6	6	6	pKd	1
Homo sapiens	Interleukin-1 receptor-associated kinase 1	5.9	5.9	5.9	pKd	1
Homo sapiens	Interleukin-1 receptor-associated kinase 1	5.1	5.1	5.1	pKi	1
Homo sapiens	Macrophage colony stimulating factor receptor	6	5.9	6.5	pIC50	3
Homo sapiens	Macrophage colony stimulating factor receptor	7.7	7.7	8	pKd	2
Homo sapiens	Macrophage colony stimulating factor receptor	6.8	6.8	6.8	pKi	1
Homo sapiens	MAP kinase p38 alpha	4	4	4.9	pIC50	2
Homo sapiens	Maternal embryonic leucine zipper kinase	5.7	5.7	5.7	pKd	2
Homo sapiens	Mixed lineage kinase 7	5.6	5.6	5.6	pKd	2
Homo sapiens	Platelet-derived growth factor receptor alpha	7.1	7.1	7.1	pEC50	1
Homo sapiens	Platelet-derived growth factor receptor alpha	7.1	6.8	8.7	pIC50	6
Homo sapiens	Platelet-derived growth factor receptor alpha	7.5	7.5	7.5	pKd	2
Homo sapiens	Platelet-derived growth factor receptor alpha	6.8	6.8	6.8	pKi	1
Homo sapiens	Platelet-derived growth factor receptor beta	6.6	6.4	7.1	pIC50	4
Homo sapiens	Platelet-derived growth factor receptor beta	7.9	7.6	7.9	pKd	3
Homo sapiens	Platelet-derived growth factor receptor beta	7.3	7.3	7.3	pKi	1
Rattus norvegicus	Platelet-derived growth factor receptor beta	6.8	6.8	6.8	pIC50	1
Homo sapiens	Serine/threonine-protein kinase 17A	5.3	5.3	5.6	pKd	3
Homo sapiens	Serine/threonine-protein kinase B-raf	5.5	5.5	5.5	pKd	2
Homo sapiens	Serine/threonine-protein kinase GAK	6	5.4	6	pKd	3
Homo sapiens	Serine/threonine-protein kinase PLK4	5.1	5.1	5.1	pKd	3
Homo sapiens	Serine/threonine-protein kinase RAF	5.8	5.8	5.8	pKd	2
Homo sapiens	Serine/threonine-protein kinase TAO1	5.4	5.4	5.4	pKi	1
Homo sapiens	Serine/threonine-protein kinase TNNI3K	5.4	5.4	5.4	pKd	2
Homo sapiens	Stem cell growth factor receptor	7	7	7	pEC50	1
Homo sapiens	Stem cell growth factor receptor	7	5	7.8	pIC50	22
Homo sapiens	Stem cell growth factor receptor	7	5.5	7.9	pKd	16
Homo sapiens	Tyrosine-protein kinase ABL	6.7	4.1	7.7	pIC50	32
Homo sapiens	Tyrosine-protein kinase ABL	7.4	5.2	9	pKd	26
Homo sapiens	Tyrosine-protein kinase ABL	7.4	5.2	7.9	pKi	6
Mus musculus	Tyrosine-protein kinase ABL	6.1	4.7	8	pIC50	3
Homo sapiens	Tyrosine-protein kinase ABL2	6.6	6.6	6.6	pIC50	1
Homo sapiens	Tyrosine-protein kinase ABL2	8	6.3	8.2	pKd	5
Homo sapiens	Tyrosine-protein kinase BLK	6.3	6.3	6.3	pKd	2
Homo sapiens	Tyrosine-protein kinase FGR	5.6	5.6	5.6	pKd	2
Homo sapiens	Tyrosine-protein kinase FRK	5.8	5.5	5.8	pKd	3
Homo sapiens	Tyrosine-protein kinase FRK	6.5	6.5	6.5	pKi	1
Homo sapiens	Tyrosine-protein kinase FYN	5.5	5.3	5.5	pKd	3
Homo sapiens	Tyrosine-protein kinase LCK	6.5	6.5	6.8	pIC50	3
Homo sapiens	Tyrosine-protein kinase LCK	7.4	7.2	7.4	pKd	3
Homo sapiens	Tyrosine-protein kinase LCK	6.5	6.5	6.5	pKi	1
Homo sapiens	Tyrosine-protein kinase Lyn	6.7	6.7	6.7	pIC50	1
Homo sapiens	Tyrosine-protein kinase Lyn	6.1	6.1	6.1	pKd	1
Homo sapiens	Tyrosine-protein kinase Lyn	6.7	6.7	6.7	pKi	1
Homo sapiens	Tyrosine-protein kinase receptor FLT3	5.2	5.2	5.2	pKd	1
Gallus gallus	Tyrosine-protein kinase SRC	5.6	5.6	5.6	pIC50	1
Homo sapiens	Tyrosine-protein kinase SRC	4.5	4.5	4.5	pKi	3
Homo sapiens	Tyrosine-protein kinase SYK	5.3	5.3	5.3	pIC50	1
Homo sapiens	Tyrosine-protein kinase SYK	5.3	5.3	5.3	pKi	2
Homo sapiens	Tyrosine-protein kinase TYK2	5.1	5.1	5.1	pKd	2
Homo sapiens	Vascular endothelial growth factor receptor 2	4.6	4.6	4.6	pIC50	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 K
593

2 T
594

3 L
595

4 G
596

5 A
597

6 G
598

7 A
599

8 F
600

9 G
601

10 K
602

11 V
603

12 V
604

13 E
605

14 V
620

15 A
621

16 V
622

17 K
623

18 M
624

19 L
625

20 A
636

•

αC

b.l

21 L
637

22 M
638

23 S
639

24 E
640

25 L
641

26 K
642

27 V
643

28 L
644

29 S
645

30 Y
646

31 L
647

32 G
648

33 M
651

34 N
652

35 I
653

36 V
654

37 N
655

38 L
656

39 L
657

40 G
658

•

hinge

linker

αD

αE

41 A
659

42 L
667

43 V
668

44 I
669

45 T
670

46 E
671

47 Y
672

48 C
673

49 C
674

50 Y
675

51 G
676

52 D
677

53 L
678

54 L
679

55 N
680

56 F
681

57 L
682

58 R
683

59 R
684

60 F
782

•

••

•

αE

c.l

VII

VIII

61 L
783

62 A
784

63 S
785

64 K
786

65 N
787

66 C
788

67 I
789

68 H
790

69 R
791

70 D
792

71 L
793

72 A
794

73 A
795

74 R
796

75 N
797

76 I
798

77 L
799

78 L
800

79 I
808

80 C
809

•

••

•

DFG

a.l

81 D
810

82 F
811

83 G
812

84 L
813

85 A
814

••

Interaction pattern search

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