KLIFS - the structural kinase database

Structure information


PDB:	1XBB
PubMed:	15507431
Release date:	2004-11-02
Resolution:	1.57 Å

Kinase:	SYK
Family:	Syk
Group:	TK
Species:	HUMAN

Quality Score:	8.1
Missing Residues:	0
Missing Atoms:	19

DFG conformation:	in
αC-helix conformation:	in
Salt bridge K^III.17 and E^αC.24:	Yes (3Å)


ASP rotation (xDFG.81) :	354°
PHE rotation (xDFG.82) :	17°
Activation loop position:	-3.6Å
αC-helix position:	17.9Å

G-rich loop angle:	60.8°
G-rich loop distance:	18.9Å
G-rich loop rotation:	50.9°

Other models from this PDB:

2D & 3D views

Binding pocket waters

The following waters were found in the defined clusters:

I2

H-bond protein

I3

H-bond ligand

H-bond protein

I4

H-bond protein

I5

H-bond ligand

H-bond protein

I10

H-bond protein

Binding pocket sequence

Uniprot	KELGSGNFGTVKKVAVKILELLAEANVMQQLDPYIVRMIGIMLVMEMAELGPLNKYLQQYLEESNFVHRDLAARNVLLISDFGLS
Structure:	KELGSGNFGTVKKVAVKILELLAEANVMQQLDPYIVRMIGIMLVMEMAELGPLNKYLQQYLEESNFVHRDLAARNVLLISDFGLS

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: STI
Ligand Name: 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE

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LABELS
KLIFS residue #
Amino Acid
None
COLORS
Interaction types
KLIFS (all res.)
KLIFS (interacting res.)
None
OTHER
Show/hide non-interacting res.
En/disable resizing interacting res.

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
375

2 E
376

3 L
377

4 G
378

5 S
379

6 G
380

7 N
381

8 F
382

9 G
383

10 T
384

11 V
385

12 K
386

13 K
387

14 V
399

15 A
400

16 V
401

17 K
402

18 I
403

19 L
404

20 E
416

■

αC

b.l

IV

21 L
417

22 L
418

23 A
419

24 E
420

25 A
421

26 N
422

27 V
423

28 M
424

29 Q
425

30 Q
426

31 L
427

32 D
428

33 P
430

34 Y
431

35 I
432

36 V
433

37 R
434

38 M
435

39 I
436

40 G
437

■

IV

V

GK

hinge

linker

αD

αE

41 I
438

42 M
445

43 L
446

44 V
447

45 M
448

46 E
449

47 M
450

48 A
451

49 E
452

50 L
453

51 G
454

52 P
455

53 L
456

54 N
457

55 K
458

56 Y
459

57 L
460

58 Q
461

59 Q
462

60 Y
484

■

■▲▲

■

αE

VI

c.l

VII

VIII

x

61 L
485

62 E
486

63 E
487

64 S
488

65 N
489

66 F
490

67 V
491

68 H
492

69 R
493

70 D
494

71 L
495

72 A
496

73 A
497

74 R
498

75 N
499

76 V
500

77 L
501

78 L
502

79 I
510

80 S
511

■

DFG

a.l

81 D
512

82 F
513

83 G
514

84 L
515

85 S
516

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL941
Bioaffinities: 254 records for 45 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Breakpoint cluster region protein	8.2	8.2	8.2	pKd	2
Homo sapiens	Casein kinase II alpha (prime)	5.4	5.4	5.4	pKd	1
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	6.7	7.8	pKd	3
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	9.1	7.7	9.2	pKd	4
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	8	7.7	8	pKd	3
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	MAP kinase p38 alpha	5.5	5.5	5.5	pKd	1
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	Phosphatidylinositol-5-phosphate 4-kinase type-2 gamma	5.4	5.4	6.4	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	6.2	8.7	pIC50	7
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	27
Homo sapiens	Stem cell growth factor receptor	7.2	5.5	7.9	pKd	17
Homo sapiens	Tyrosine-protein kinase ABL	6.7	4.1	7.7	pIC50	34
Homo sapiens	Tyrosine-protein kinase ABL	7.4	5.2	9	pKd	28
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	7
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	4
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	6.9	6.9	6.9	pIC50	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	4.4	4.4	4.4	pKd	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

1XBB - chain A (model B) | Spleen tyrosine kinase

Structure information

2D & 3D views

Binding pocket waters

Binding pocket sequence

Modified residues

Orthosteric ligand

Kinase-ligand interactions

Interaction pattern search

Binding affinities