5N23 - chain A (model A) | Protein kinase cAMP-activated catalytic subunit alpha
Structure information
PDB: | 5N23 |
PubMed: | - |
Release date: | 2018-03-14 |
Resolution: | 2.09 Å |
Kinase: | PRKACA (PKACa) |
Family: | PKA |
Group: | AGC |
Species: | HUMAN |
Quality Score: | 8 |
Missing Residues: | 0 |
Missing Atoms: | 0 |
DFG conformation: | in |
αC-helix conformation: | in |
Salt bridge KIII.17 and EαC.24: | Yes (2.9Å) |
ASP rotation (xDFG.81) : | 350° |
PHE rotation (xDFG.82) : | 4° |
Activation loop position: | -4Å |
αC-helix position: | 17.5Å |
G-rich loop angle: | 59.5° |
G-rich loop distance: | 17.5Å |
G-rich loop rotation: | 86.4° |
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 | KTLGTGSFGRVMLYAMKILHTLNEKRILQAVNPFLVKLEFSYMVMEYVPGGEMFSHLRRYLHSLDLIYRDLKPENLLIVTDFGFA |
Structure: | RTLGTGSFGRVMLYAMKILHTLNEKRIQQAVNPFLVKLEFSYMVLEYAPGGEMFSHLRRYLHSLDLIYRDLKPENLLIVADFGFA |
Modified residues
Residue 10 (not in pocket)
Phosphorylated serine
Residue 139 (not in pocket)
Phosphorylated serine
Residue 197 (not in pocket)
Phosphorylated threonine
Residue 338 (not in pocket)
Phosphorylated serine
Orthosteric ligand
Ligand HET-code: 35R
Ligand Name: 1-cyclopropyl-3-{3-[5-(morpholin-4-ylmethyl)-1H-benzimidazol-2-yl]-1H-pyrazol-4-yl}urea
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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 R 47 | 2 T 48 | 3 L 49 | 4 G 50 | 5 T 51 | 6 G 52 | 7 S 53 | 8 F 54 | 9 G 55 | 10 R 56 | 11 V 57 | 12 M 58 | 13 L 59 | 14 Y 69 | 15 A 70 | 16 M 71 | 17 K 72 | 18 I 73 | 19 L 74 | 20 H 87 |
■ | ■ | ■ | ■ | ||||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 T 88 | 22 L 89 | 23 N 90 | 24 E 91 | 25 K 92 | 26 R 93 | 27 I 94 | 28 Q 95 | 29 Q 96 | 30 A 97 | 31 V 98 | 32 N 99 | 33 P 101 | 34 F 102 | 35 L 103 | 36 V 104 | 37 K 105 | 38 L 106 | 39 E 107 | 40 F 108 |
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 S 109 | 42 Y 117 | 43 M 118 | 44 V 119 | 45 L 120 | 46 E 121 | 47 Y 122 | 48 A 123 | 49 P 124 | 50 G 125 | 51 G 126 | 52 E 127 | 53 M 128 | 54 F 129 | 55 S 130 | 56 H 131 | 57 L 132 | 58 R 133 | 59 R 134 | 60 Y 156 |
■ | ▲ | ■♦ | ▲▲ | ■ | ■ | ■ | ■ | ■▲ | |||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 L 157 | 62 H 158 | 63 S 159 | 64 L 160 | 65 D 161 | 66 L 162 | 67 I 163 | 68 Y 164 | 69 R 165 | 70 D 166 | 71 L 167 | 72 K 168 | 73 P 169 | 74 E 170 | 75 N 171 | 76 L 172 | 77 L 173 | 78 I 174 | 79 V 182 | 80 A 183 |
■ | |||||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 184 | 82 F 185 | 83 G 186 | 84 F 187 | 85 A 188 | |||||||||||||||
Binding affinities
ChEMBL ID:CHEMBL495727Bioaffinities: 166 records for 123 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Activin receptor type-1 | 7.1 | 7.1 | 7.1 | pKd | 1 |
Homo sapiens | Activin receptor type-1B | 6.1 | 6.1 | 6.1 | pKd | 1 |
Homo sapiens | Adaptor-associated kinase | 7.8 | 7.8 | 7.8 | pKd | 1 |
Homo sapiens | AMP-activated protein kinase, alpha-1 subunit | 7.3 | 7.3 | 7.3 | pKd | 1 |
Homo sapiens | AMP-activated protein kinase, gamma-1 subunit | 7.5 | 7.5 | 7.5 | pKd | 1 |
Homo sapiens | AMP-activated protein kinase, gamma-2 subunit | 7.2 | 7.2 | 7.2 | pKd | 1 |
Homo sapiens | BMP-2-inducible protein kinase | 7.5 | 7.5 | 7.5 | pKd | 1 |
Homo sapiens | Bone morphogenetic protein receptor type-1A | 6.4 | 6.4 | 6.4 | pKd | 1 |
Homo sapiens | Bone morphogenetic protein receptor type-1B | 7.7 | 7.7 | 7.7 | pKd | 1 |
Homo sapiens | Bone morphogenetic protein receptor type-2 | 7.4 | 7.4 | 7.4 | pKd | 1 |
Homo sapiens | Breakpoint cluster region protein | 6.8 | 6.8 | 6.8 | pKd | 2 |
Homo sapiens | cAMP-dependent protein kinase alpha-catalytic subunit | 5.5 | 5.5 | 5.5 | pKd | 1 |
Homo sapiens | cAMP-dependent protein kinase beta-1 catalytic subunit | 6 | 6 | 6 | pKd | 1 |
Homo sapiens | cAMP-dependent protein kinase, gamma catalytic subunit | 8.5 | 8.5 | 8.5 | pKd | 1 |
Homo sapiens | Casein kinase II alpha (prime) | 7.2 | 7.2 | 7.2 | pKd | 1 |
Homo sapiens | Cell division cycle 7-related protein kinase | 6.3 | 6.3 | 6.3 | pKd | 1 |
Homo sapiens | c-Jun N-terminal kinase 1 | 6.8 | 6.8 | 6.8 | pKd | 1 |
Homo sapiens | c-Jun N-terminal kinase 2 | 6.3 | 6.3 | 6.3 | pKd | 1 |
Homo sapiens | c-Jun N-terminal kinase 3 | 6.5 | 6.5 | 6.5 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 10 | 8.1 | 8.1 | 8.1 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 4 | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 5 | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 6 | 6.9 | 6.9 | 6.9 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 9 | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Dual specificity mitogen-activated protein kinase kinase 5 | 7.3 | 7.3 | 7.3 | pKd | 1 |
Homo sapiens | Dual specificity mitogen-activated protein kinase kinase 6 | 5.5 | 5.5 | 5.5 | pKd | 1 |
Homo sapiens | Dual-specificity tyrosine-phosphorylation regulated kinase 1A | 5.6 | 5.6 | 5.6 | pKd | 1 |
Homo sapiens | Dual specificty protein kinase CLK1 | 5.7 | 5.7 | 5.7 | pKd | 1 |
Homo sapiens | Ephrin type-A receptor 2 | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Ephrin type-A receptor 4 | 4.4 | 4.4 | 4.4 | pKd | 1 |
Homo sapiens | Ephrin type-A receptor 7 | 8.1 | 8.1 | 8.1 | pKd | 1 |
Homo sapiens | Ephrin type-B receptor 6 | 7.9 | 7.9 | 7.9 | pKd | 1 |
Homo sapiens | Fibroblast growth factor receptor 1 | 8 | 8 | 8 | pIC50 | 2 |
Homo sapiens | Fibroblast growth factor receptor 1 | 7.6 | 7.6 | 7.6 | pKd | 1 |
Homo sapiens | Fibroblast growth factor receptor 2 | 8 | 8 | 9 | pIC50 | 2 |
Homo sapiens | Fibroblast growth factor receptor 3 | 8 | 8 | 8 | pIC50 | 1 |
Homo sapiens | Glycogen synthase kinase-3 alpha | 8.2 | 8.2 | 8.2 | pKd | 1 |
Homo sapiens | Glycogen synthase kinase-3 beta | 9 | 9 | 9 | pIC50 | 1 |
Homo sapiens | Glycogen synthase kinase-3 beta | 8.2 | 8.2 | 8.2 | pKd | 1 |
Homo sapiens | G protein-coupled receptor kinase 6 | 4.9 | 4.9 | 4.9 | pKd | 1 |
Homo sapiens | Hepatocyte growth factor receptor | 8.2 | 8.2 | 8.2 | pKd | 1 |
Homo sapiens | Inhibitor of nuclear factor kappa B kinase epsilon subunit | 6.7 | 6.7 | 6.7 | pKd | 1 |
Homo sapiens | LIM domain kinase 1 | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | LIM domain kinase 2 | 5.4 | 5.4 | 5.4 | pKd | 1 |
Homo sapiens | MAP kinase-activated protein kinase 5 | 6.2 | 6.2 | 6.2 | pKd | 1 |
Homo sapiens | MAP/microtubule affinity-regulating kinase 2 | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Maternal embryonic leucine zipper kinase | 6.2 | 6.2 | 6.2 | pIC50 | 1 |
Homo sapiens | Maternal embryonic leucine zipper kinase | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase 1 | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase 11 | 7.3 | 7.3 | 7.3 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase 2 | 6.6 | 6.6 | 6.6 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase 3 | 6.5 | 6.5 | 6.5 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase 5 | 4.6 | 4.6 | 4.6 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 1 | 6.7 | 6.7 | 6.7 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 4 | 7 | 7 | 7 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 5 | 5.7 | 5.7 | 5.7 | pKd | 1 |
Homo sapiens | Mitotic checkpoint serine/threonine-protein kinase BUB1 | 7 | 7 | 7 | pKd | 1 |
Homo sapiens | Myosin light chain kinase | 6.9 | 6.9 | 6.9 | pKd | 1 |
Homo sapiens | Platelet-derived growth factor receptor alpha | 8 | 8 | 8 | pIC50 | 1 |
Homo sapiens | Protein kinase C alpha | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Protein kinase C beta | 5.5 | 5.5 | 5.5 | pKd | 1 |
Homo sapiens | Protein kinase C mu | 8 | 8 | 8 | pIC50 | 1 |
Homo sapiens | Protein kinase C nu | 6.3 | 6.3 | 6.3 | pKd | 1 |
Homo sapiens | Protein kinase N1 | 5.5 | 5.5 | 5.5 | pKd | 1 |
Homo sapiens | Protein kinase N2 | 5.6 | 5.6 | 5.6 | pKd | 1 |
Homo sapiens | Proto-oncogene tyrosine-protein kinase MER | 9 | 9 | 9 | pIC50 | 1 |
Homo sapiens | Pyruvate dehydrogenase kinase isoform 1 | 8 | 8 | 8 | pIC50 | 1 |
Homo sapiens | Ribosomal protein S6 kinase 1 | 6.9 | 6.9 | 6.9 | pKd | 1 |
Homo sapiens | Ribosomal protein S6 kinase alpha 1 | 6.3 | 6.3 | 6.3 | pKd | 2 |
Homo sapiens | Ribosomal protein S6 kinase alpha 2 | 9 | 9 | 9 | pIC50 | 2 |
Homo sapiens | Ribosomal protein S6 kinase alpha 3 | 9 | 9 | 9 | pIC50 | 2 |
Homo sapiens | Ribosomal protein S6 kinase alpha 3 | 7 | 7 | 7 | pKd | 2 |
Homo sapiens | Ribosomal protein S6 kinase alpha 4 | 8 | 8 | 8 | pIC50 | 2 |
Homo sapiens | Ribosomal protein S6 kinase alpha 4 | 7.1 | 7.1 | 7.1 | pKd | 2 |
Homo sapiens | Ribosomal protein S6 kinase alpha 5 | 5.9 | 5.9 | 5.9 | pKd | 2 |
Homo sapiens | Ribosomal protein S6 kinase alpha 6 | 7.8 | 7.8 | 7.8 | pKd | 2 |
Homo sapiens | Serine/threonine-protein kinase 10 | 7.1 | 7.1 | 7.1 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase 16 | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase 17A | 8 | 8 | 8 | pIC50 | 1 |
Homo sapiens | Serine/threonine-protein kinase 2 | 6.4 | 6.4 | 6.4 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase Aurora-A | 8.5 | 8.5 | 8.5 | pIC50 | 2 |
Homo sapiens | Serine/threonine-protein kinase Aurora-A | 7.3 | 7.3 | 7.8 | pKd | 2 |
Homo sapiens | Serine/threonine-protein kinase Aurora-B | 7.5 | 7.5 | 8.6 | pIC50 | 4 |
Homo sapiens | Serine/threonine-protein kinase Aurora-B | 7.8 | 7.8 | 7.8 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase Chk1 | 7.1 | 7.1 | 7.1 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase c-TAK1 | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase D2 | 6.6 | 6.6 | 6.6 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase GAK | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase LATS1 | 7.4 | 7.4 | 7.4 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase Nek3 | 5.7 | 5.7 | 5.7 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase NEK9 | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase PAK 4 | 7 | 7 | 7 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase PAK6 | 6.7 | 6.7 | 6.7 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase PCTAIRE-1 | 7.5 | 7.5 | 7.5 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase PCTAIRE-2 | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase PLK4 | 7.7 | 7.7 | 7.7 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase receptor R3 | 7.8 | 7.8 | 7.8 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase SIK2 | 7.5 | 7.5 | 7.5 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase SIK3 | 5.4 | 5.4 | 5.4 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase TAO1 | 5.7 | 5.7 | 5.7 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase TBK1 | 7 | 7 | 7 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase ULK3 | 7.4 | 7.4 | 7.4 | pKd | 1 |
Homo sapiens | TGF-beta receptor type I | 7.1 | 7.1 | 7.1 | pKd | 1 |
Homo sapiens | TGF-beta receptor type II | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | TRAF2- and NCK-interacting kinase | 6.1 | 6.1 | 6.1 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase ABL | 8.4 | 8 | 8.4 | pIC50 | 3 |
Homo sapiens | Tyrosine-protein kinase ABL | 6.5 | 6.5 | 6.5 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase ABL2 | 6 | 6 | 6 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase BRK | 6.7 | 6.7 | 6.7 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase BTK | 6.3 | 6.3 | 6.3 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase CSK | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase FER | 6.5 | 6.5 | 6.5 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase FGR | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase FYN | 6.3 | 6.3 | 6.3 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase HCK | 6.2 | 6.2 | 6.2 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase JAK1 | 6.4 | 6.4 | 6.4 | pKd | 2 |
Homo sapiens | Tyrosine-protein kinase JAK2 | 8.9 | 8.9 | 9 | pIC50 | 4 |
Homo sapiens | Tyrosine-protein kinase JAK2 | 8 | 8 | 8 | pKd | 2 |
Homo sapiens | Tyrosine-protein kinase JAK3 | 9 | 9 | 9 | pIC50 | 4 |
Homo sapiens | Tyrosine-protein kinase LCK | 6.1 | 6.1 | 6.1 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase Lyn | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase receptor FLT3 | 8 | 8 | 8 | pIC50 | 2 |
Homo sapiens | Tyrosine-protein kinase receptor FLT3 | 7.2 | 7.2 | 7.2 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase receptor RET | 9 | 9 | 9 | pIC50 | 1 |
Homo sapiens | Tyrosine-protein kinase receptor RET | 8 | 8 | 8 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase SRC | 8 | 8 | 8 | pIC50 | 1 |
Homo sapiens | Tyrosine-protein kinase SRC | 6.2 | 6.2 | 6.2 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase SYK | 6.9 | 6.9 | 6.9 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase TEC | 6.9 | 6.9 | 6.9 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase TYK2 | 9 | 9 | 9 | pIC50 | 2 |
Homo sapiens | Tyrosine-protein kinase TYK2 | 6.6 | 6.6 | 6.6 | pKd | 2 |
Homo sapiens | Tyrosine-protein kinase YES | 9 | 9 | 9 | pIC50 | 1 |
Homo sapiens | Tyrosine-protein kinase YES | 6.2 | 6.2 | 6.2 | pKd | 1 |
Homo sapiens | Uncharacterized aarF domain-containing protein kinase 1 | 6.3 | 6.3 | 6.3 | pKd | 1 |
Homo sapiens | Vascular endothelial growth factor receptor 1 | 8 | 8 | 8 | pIC50 | 1 |
Homo sapiens | Vascular endothelial growth factor receptor 2 | 8 | 8 | 8 | pIC50 | 1 |
Homo sapiens | Vascular endothelial growth factor receptor 3 | 9 | 9 | 9 | pIC50 | 1 |