KLIFS - the structural kinase database

Structure information


PDB:	6BG2
PubMed:	-
Release date:	2018-10-31
Resolution:	1.83 Å

Kinase:	PRKG1 (PKG1)
Family:	PKG
Group:	AGC
Species:	HUMAN

Quality Score:	9.6
Missing Residues:	0
Missing Atoms:	4

DFG conformation:	in
αC-helix conformation:	in
Salt bridge K^III.17 and E^αC.24:	Yes (2.7Å)


ASP rotation (xDFG.81) :	340°
PHE rotation (xDFG.82) :	17°
Activation loop position:	-4Å
αC-helix position:	17.3Å

G-rich loop angle:	50.7°
G-rich loop distance:	15.2Å
G-rich loop rotation:	54.6°

Other models from this PDB:

2D & 3D views

Binding pocket waters

The following waters were found in the defined clusters:

I1

H-bond protein

I4

H-bond protein

Binding pocket sequence

Uniprot	DTLGVGGFGRVELFAMKILHIRSEKQIMQGAHDFIVRLYRTYMLMEACLGGELWTILRDYLHSKGIIYRDLKPENLILLVDFGFA
Structure:	DTLGVGGFGRVELFAMKILHIRSEKQIMQGAHDFIVRLYRTYMLMEACLGGELWTILRDYLHSKGIIYRDLKPENLILLVDFGFA

Modified residues

Residue 517 (not in pocket)

Phosphorylated threonine

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 D
364

2 T
365

3 L
366

4 G
367

5 V
368

6 G
369

7 G
370

8 F
371

9 G
372

10 R
373

11 V
374

12 E
375

13 L
376

14 F
387

15 A
388

16 M
389

17 K
390

18 I
391

19 L
392

20 H
405

■

▲

▲▲

▲

■

▲

αC

b.l

IV

21 I
406

22 R
407

23 S
408

24 E
409

25 K
410

26 Q
411

27 I
412

28 M
413

29 Q
414

30 G
415

31 A
416

32 H
417

33 D
419

34 F
420

35 I
421

36 V
422

37 R
423

38 L
424

39 Y
425

40 R
426

IV

V

GK

hinge

linker

αD

αE

41 T
427

42 Y
435

43 M
436

44 L
437

45 M
438

46 E
439

47 A
440

48 C
441

49 L
442

50 G
443

51 G
444

52 E
445

53 L
446

54 W
447

55 T
448

56 I
449

57 L
450

58 R
451

59 D
452

60 Y
474

■

▲

■▲

αE

VI

c.l

VII

VIII

x

61 L
475

62 H
476

63 S
477

64 K
478

65 G
479

66 I
480

67 I
481

68 Y
482

69 R
483

70 D
484

71 L
485

72 K
486

73 P
487

74 E
488

75 N
489

76 L
490

77 I
491

78 L
492

79 L
500

80 V
501

▲

■

DFG

a.l

81 D
502

82 F
503

83 G
504

84 F
505

85 A
506

▲●

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).

6BG2 - chain C (model A) | Protein kinase, cGMP-dependent, type I