6BG2 - chain D (model A) | Protein kinase, cGMP-dependent, type I
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: | 9.4 |
Missing Residues: | 0 |
Missing Atoms: | 6 |
DFG conformation: | in |
αC-helix conformation: | in |
Salt bridge KIII.17 and EαC.24: | Yes (2.6Å) |
ASP rotation (xDFG.81) : | 340° |
PHE rotation (xDFG.82) : | 16° |
Activation loop position: | -3.9Å |
αC-helix position: | 17.3Å |
G-rich loop angle: | 50.1° |
G-rich loop distance: | 14.9Å |
G-rich loop rotation: | 53.8° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I1
No H-bonds
I4
H-bond protein
I5
H-bond protein
I11
H-bond ligand
Binding pocket sequence
Uniprot | DTLGVGGFGRVELFAMKILHIRSEKQIMQGAHDFIVRLYRTYMLMEACLGGELWTILRDYLHSKGIIYRDLKPENLILLVDFGFA |
Structure: | DTLGVGGFGRVELFAMKILHIRSEKQIMQGAHDFIVRLYRTYMLMEACLGGELWTILRDYLHSKGIIYRDLKPENLILLVDFGFA |
Modified residues
Residue 517 (not in pocket)
Phosphorylated threonine
Orthosteric ligand
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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 | |||||||||||||||
▲ |
Binding affinities
ChEMBL ID:CHEMBL1230989Bioaffinities: No (p)Ki/(p)IC50/(p)EC50 values for kinases found (with a ChEMBL confidence ≥ 8).