KLIFS - the structural kinase database

Structure information


PDB:	3KN5
PubMed:	20382163
Release date:	2010-04-21
Resolution:	2.4 Å

Kinase:	RPS6KA5-b (MSK1-b)
Family:	RSKb
Group:	CAMK
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 (2.7Å)


ASP rotation (xDFG.81) :	337°
PHE rotation (xDFG.82) :	2°
Activation loop position:	-3.7Å
αC-helix position:	18.4Å

G-rich loop angle:	54.7°
G-rich loop distance:	16.8Å
G-rich loop rotation:	49.5°

Other models from this PDB:

2D & 3D views

Binding pocket waters

The following waters were found in the defined clusters:

I4

H-bond protein

Binding pocket sequence

Uniprot	KPLGEGSFSICRKFAVKIINTQKEITALKLCEPNIVKLHEVFLVMELLNGGELFERIKKHMHDVGVVHRDLKPENLLFIIDFGFA
Structure:	KPLGEGSFSICRKFAVKIINTQKEITALKLCEPNIVKLHEVFLVMELLNGGELFERIKKHMHDVGVVHRDLKPENLLFIIDFGFA

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: ANP
Ligand Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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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
430

2 P
431

3 L
432

4 G
433

5 E
434

6 G
435

7 S
436

8 F
437

9 S
438

10 I
439

11 C
440

12 R
441

13 K
442

14 F
452

15 A
453

16 V
454

17 K
455

18 I
456

19 I
457

20 N
464

■

▲

■

αC

b.l

IV

21 T
465

22 Q
466

23 K
467

24 E
468

25 I
469

26 T
470

27 A
471

28 L
472

29 K
473

30 L
474

31 C
475

32 E
476

33 P
479

34 N
480

35 I
481

36 V
482

37 K
483

38 L
484

39 H
485

40 E
486

IV

V

GK

hinge

linker

αD

αE

41 V
487

42 F
495

43 L
496

44 V
497

45 M
498

46 E
499

47 L
500

48 L
501

49 N
502

50 G
503

51 G
504

52 E
505

53 L
506

54 F
507

55 E
508

56 R
509

57 I
510

58 K
511

59 K
512

60 H
534

▲

■

■▲

αE

VI

c.l

VII

VIII

x

61 M
535

62 H
536

63 D
537

64 V
538

65 G
539

66 V
540

67 V
541

68 H
542

69 R
543

70 D
544

71 L
545

72 K
546

73 P
547

74 E
548

75 N
549

76 L
550

77 L
551

78 F
552

79 I
563

80 I
564

■

DFG

a.l

81 D
565

82 F
566

83 G
567

84 F
568

85 A
569

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL1230989

Bioaffinities: No (p)K_i/(p)IC₅₀/(p)EC₅₀ values for kinases found (with a ChEMBL confidence ≥ 8).

3KN5 - chain B | Ribosomal protein S6 kinase A5 (2nd domain)