KLIFS - the structural kinase database

Structure information


PDB:	3ET7
PubMed:	18951788
Release date:	2009-06-23
Resolution:	2.7 Å

Kinase:	PTK2B (PYK2)
Family:	FAK
Group:	TK
Species:	HUMAN

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

DFG conformation:	out-like
αC-helix conformation:	in
Salt bridge K^III.17 and E^αC.24:	Yes (3.1Å)


ASP rotation (xDFG.81) :	89°
PHE rotation (xDFG.82) :	160°
Activation loop position:	-1.1Å
αC-helix position:	17.7Å

G-rich loop angle:	56.4°
G-rich loop distance:	16.9Å
G-rich loop rotation:	90.6°

2D & 3D views

Binding pocket waters

No waters were found in the defined clusters

Binding pocket sequence

Uniprot	RILGEGFFGEVYEVAVKTCKFMSEAVIMKNLDPHIVKLIGIWIIMELYPYGELGHYLERYLESINCVHRDIAVRNILVLGDFGLS
Structure:	RILGEGFFGEVYEVAVKTCKFMSEAVIMKNLDPHIVKLIGIWIIMELYPYGELGHYLERYLESINCVHRDIAVRNILVLGDFGLS

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: 349
Ligand Name: 5-{[4-{[2-(pyrrolidin-1-ylsulfonyl)benzyl]amino}-5-(trifluoromethyl)pyrimidin-2-yl]amino}-1,3-dihydro-2H-indol-2-one

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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 R
429

2 I
430

3 L
431

4 G
432

5 E
433

6 G
434

7 F
435

8 F
436

9 G
437

10 E
438

11 V
439

12 Y
440

13 E
441

14 V
454

15 A
455

16 V
456

17 K
457

18 T
458

19 C
459

20 K
470

■

αC

b.l

IV

21 F
471

22 M
472

23 S
473

24 E
474

25 A
475

26 V
476

27 I
477

28 M
478

29 K
479

30 N
480

31 L
481

32 D
482

33 P
484

34 H
485

35 I
486

36 V
487

37 K
488

38 L
489

39 I
490

40 G
491

■

IV

V

GK

hinge

linker

αD

αE

41 I
492

42 W
499

43 I
500

44 I
501

45 M
502

46 E
503

47 L
504

48 Y
505

49 P
506

50 Y
507

51 G
508

52 E
509

53 L
510

54 G
511

55 H
512

56 Y
513

57 L
514

58 E
515

59 R
516

60 Y
539

■

■♦▲▲

■

αE

VI

c.l

VII

VIII

x

61 L
540

62 E
541

63 S
542

64 I
543

65 N
544

66 C
545

67 V
546

68 H
547

69 R
548

70 D
549

71 I
550

72 A
551

73 V
552

74 R
553

75 N
554

76 I
555

77 L
556

78 V
557

79 L
565

80 G
566

■

DFG

a.l

81 D
567

82 F
568

83 G
569

84 L
570

85 S
571

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL529889
Bioaffinities: 2 records for 2 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Focal adhesion kinase 1	6.8	6.8	6.8	pIC50	1
Homo sapiens	Protein tyrosine kinase 2 beta	7.8	7.8	7.8	pIC50	1

3ET7 - chain A | Protein tyrosine kinase 2 beta