KLIFS - the structural kinase database

Structure information


PDB:	3HMM
PubMed:	19285388
Release date:	2009-06-23
Resolution:	1.7 Å

Kinase:	TGFBR1 (TGFbR1)
Family:	STKR
Group:	TKL
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) :	340°
PHE rotation (xDFG.82) :	357°
Activation loop position:	-3.4Å
αC-helix position:	17.3Å

G-rich loop angle:	51°
G-rich loop distance:	15.2Å
G-rich loop rotation:	72.5°

2D & 3D views

Binding pocket waters

The following waters were found in the defined clusters:

I1

H-bond protein

I2

H-bond protein

I5

H-bond ligand

H-bond protein

I9

H-bond ligand

Binding pocket sequence

Uniprot	ESIGKGRFGEVWRVAVKIFSWFREAEIYQTVMENILGFIAAWLVSDYHEHGSLFDYLNRTQGKPAIAHRDLKSKNILVIADLGLA
Structure:	ESIGKGRFGEVWRVAVKIFSWFREAEIYQTVMENILGFIAAWLVSDYHEHGSLFDYLNRTQGKPAIAHRDLKSKNILVIADLGLA

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: 855
Ligand Name: 2-(6-methylpyridin-2-yl)-N-pyridin-4-ylquinazolin-4-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 E
9

2 S
10

3 I
11

4 G
12

5 K
13

6 G
14

7 R
15

8 F
16

9 G
17

10 E
18

11 V
19

12 W
20

13 R
21

14 V
29

15 A
30

16 V
31

17 K
32

18 I
33

19 F
34

20 S
41

■

■▲

αC

b.l

IV

21 W
42

22 F
43

23 R
44

24 E
45

25 A
46

26 E
47

27 I
48

28 Y
49

29 Q
50

30 T
51

31 V
52

32 M
53

33 E
57

34 N
58

35 I
59

36 L
60

37 G
61

38 F
62

39 I
63

40 A
64

■

IV

V

GK

hinge

linker

αD

αE

41 A
65

42 W
77

43 L
78

44 V
79

45 S
80

46 D
81

47 Y
82

48 H
83

49 E
84

50 H
85

51 G
86

52 S
87

53 L
88

54 F
89

55 D
90

56 Y
91

57 L
92

58 N
93

59 R
94

60 T
123

■

■♦

■▲

■

αE

VI

c.l

VII

VIII

x

61 Q
124

62 G
125

63 K
126

64 P
127

65 A
128

66 I
129

67 A
130

68 H
131

69 R
132

70 D
133

71 L
134

72 K
135

73 S
136

74 K
137

75 N
138

76 I
139

77 L
140

78 V
141

79 I
149

80 A
150

■

DFG

a.l

81 D
151

82 L
152

83 G
153

84 L
154

85 A
155

■

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL570533
Bioaffinities: 3 records for 2 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	MAP kinase p38 alpha	5.2	5.2	5.2	pIC50	1
Homo sapiens	TGF-beta receptor type I	7	7	7.6	pIC50	2

3HMM - chain A | Transforming growth factor beta receptor I

Structure information

2D & 3D views

Binding pocket waters

Binding pocket sequence

Modified residues

Orthosteric ligand

Kinase-ligand interactions

Interaction pattern search

Binding affinities