KLIFS - the structural kinase database

Structure information


PDB:	3POZ
PubMed:	21454582
Release date:	2011-03-30
Resolution:	1.5 Å

Kinase:	EGFR
Family:	EGFR
Group:	TK
Species:	HUMAN

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

DFG conformation:	in
αC-helix conformation:	out
Salt bridge K^III.17 and E^αC.24:	No (14.6Å)


ASP rotation (xDFG.81) :	346°
PHE rotation (xDFG.82) :	328°
Activation loop position:	-4.8Å
αC-helix position:	21Å

G-rich loop angle:	53.4°
G-rich loop distance:	16.8Å
G-rich loop rotation:	31.1°

2D & 3D views

Binding pocket waters

The following waters were found in the defined clusters:

I3

H-bond ligand

H-bond protein

I6

H-bond ligand

Binding pocket sequence

Uniprot	KVLGSGAFGTVYKVAIKELEILDEAYVMASVDPHVCRLLGIQLITQLMPFGCLLDYVREYLEDRRLVHRDLAARNVLVITDFGLA
Structure:	KVLGSGAFGTVYKVAIKELEILDEAYVMASVDPHVCRLLGIQLITQLMPFGCLLDYVREYLEDRRLVHRDLAARNVLVITDFGLA

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: 03P
Ligand Name: N-{2-[4-({3-chloro-4-[3-(trifluoromethyl)phenoxy]phenyl}amino)-5H-pyrrolo[3,2-d]pyrimidin-5-yl]ethyl}-3-hydroxy-3-methylbutanamide

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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 K
716

2 V
717

3 L
718

4 G
719

5 S
720

6 G
721

7 A
722

8 F
723

9 G
724

10 T
725

11 V
726

12 Y
727

13 K
728

14 V
742

15 A
743

16 I
744

17 K
745

18 E
746

19 L
747

20 E
758

■

αC

b.l

IV

21 I
759

22 L
760

23 D
761

24 E
762

25 A
763

26 Y
764

27 V
765

28 M
766

29 A
767

30 S
768

31 V
769

32 D
770

33 P
772

34 H
773

35 V
774

36 C
775

37 R
776

38 L
777

39 L
778

40 G
779

■

IV

V

GK

hinge

linker

αD

αE

41 I
780

42 Q
787

43 L
788

44 I
789

45 T
790

46 Q
791

47 L
792

48 M
793

49 P
794

50 F
795

51 G
796

52 C
797

53 L
798

54 L
799

55 D
800

56 Y
801

57 V
802

58 R
803

59 E
804

60 Y
827

■

■▲

■

αE

VI

c.l

VII

VIII

x

61 L
828

62 E
829

63 D
830

64 R
831

65 R
832

66 L
833

67 V
834

68 H
835

69 R
836

70 D
837

71 L
838

72 A
839

73 A
840

74 R
841

75 N
842

76 V
843

77 L
844

78 V
845

79 I
853

80 T
854

■

DFG

a.l

81 D
855

82 F
856

83 G
857

84 L
858

85 A
859

■

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL1614725
Bioaffinities: 20 records for 13 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Bone morphogenetic protein receptor type-1B	5.8	5.8	5.8	pKd	1
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 1	6	6	6	pIC50	1
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 5	5.2	5.2	5.2	pIC50	1
Homo sapiens	Ephrin type-B receptor 6	5.7	5.7	5.7	pKd	1
Homo sapiens	Epidermal growth factor receptor erbB1	7.6	5.1	9	pIC50	4
Homo sapiens	Epidermal growth factor receptor erbB1	6.2	6.2	6.2	pKd	1
Homo sapiens	Hepatocyte growth factor receptor	5.4	5.4	5.4	pIC50	1
Homo sapiens	Receptor protein-tyrosine kinase erbB-2	7.8	7.8	8.5	pIC50	4
Homo sapiens	Receptor protein-tyrosine kinase erbB-4	6.6	6.6	6.6	pIC50	1
Homo sapiens	Serine/threonine-protein kinase Aurora-B	5.8	5.8	5.8	pIC50	1
Homo sapiens	Serine/threonine protein kinase NLK	6.1	6.1	6.1	pKd	1
Homo sapiens	Tyrosine-protein kinase CSK	5.3	5.3	5.3	pIC50	1
Homo sapiens	Tyrosine-protein kinase LCK	5.6	5.6	5.6	pIC50	1
Homo sapiens	Tyrosine-protein kinase Lyn	5.3	5.3	5.3	pIC50	1

3POZ - chain A | Epidermal growth factor receptor