4WB7 - chain A (model B) | Protein kinase cAMP-activated catalytic subunit alpha
Structure information
PDB: | 4WB7 |
PubMed: | 25605907 |
Release date: | 2015-01-21 |
Resolution: | 1.9 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 (2.8Å) |
ASP rotation (xDFG.81) : | 334° |
PHE rotation (xDFG.82) : | 11° |
Activation loop position: | -4Å |
αC-helix position: | 17.5Å |
G-rich loop angle: | 48.4° |
G-rich loop distance: | 14.6Å |
G-rich loop rotation: | 59.8° |
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
I11
H-bond ligand
H-bond protein
Binding pocket sequence
Uniprot | KTLGTGSFGRVMLYAMKILHTLNEKRILQAVNPFLVKLEFSYMVMEYVPGGEMFSHLRRYLHSLDLIYRDLKPENLLIVTDFGFA |
Structure: | KTLGTGSFGRVMLYAMKILHTLNEKRILQAVNPFLVKLEFSYMVMEYVPGGEMFSHLRRYLHSLDLIYRDLKPENLLIVTDFGFA |
Modified residues
Residue 194 (not in pocket)
Phosphorylated serine
Residue 252 (not in pocket)
Phosphorylated threonine
Residue 393 (not in pocket)
Phosphorylated serine
Orthosteric ligand
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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.
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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 102 | 2 T 103 | 3 L 104 | 4 G 105 | 5 T 106 | 6 G 107 | 7 S 108 | 8 F 109 | 9 G 110 | 10 R 111 | 11 V 112 | 12 M 113 | 13 L 114 | 14 Y 124 | 15 A 125 | 16 M 126 | 17 K 127 | 18 I 128 | 19 L 129 | 20 H 142 |
■ | ■ | ■ | ▲ | ▲ | ▲ | ■ | ■ | ▲● | |||||||||||
αC | b.l | IV | |||||||||||||||||
21 T 143 | 22 L 144 | 23 N 145 | 24 E 146 | 25 K 147 | 26 R 148 | 27 I 149 | 28 L 150 | 29 Q 151 | 30 A 152 | 31 V 153 | 32 N 154 | 33 P 156 | 34 F 157 | 35 L 158 | 36 V 159 | 37 K 160 | 38 L 161 | 39 E 162 | 40 F 163 |
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 S 164 | 42 Y 172 | 43 M 173 | 44 V 174 | 45 M 175 | 46 E 176 | 47 Y 177 | 48 V 178 | 49 P 179 | 50 G 180 | 51 G 181 | 52 E 182 | 53 M 183 | 54 F 184 | 55 S 185 | 56 H 186 | 57 L 187 | 58 R 188 | 59 R 189 | 60 Y 211 |
■ | ▲ | ■ | ■▲ | ■▲ | |||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 L 212 | 62 H 213 | 63 S 214 | 64 L 215 | 65 D 216 | 66 L 217 | 67 I 218 | 68 Y 219 | 69 R 220 | 70 D 221 | 71 L 222 | 72 K 223 | 73 P 224 | 74 E 225 | 75 N 226 | 76 L 227 | 77 L 228 | 78 I 229 | 79 V 237 | 80 T 238 |
▲● | ▲ | ■ | ■▲ | ||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 239 | 82 F 240 | 83 G 241 | 84 F 242 | 85 A 243 | |||||||||||||||
Binding affinities
ChEMBL ID:CHEMBL14249Bioaffinities: 8 records for 3 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | MAP kinase-activated protein kinase 2 | 5.2 | 4.9 | 5.6 | pIC50 | 3 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase 7 | 5.6 | 5.6 | 5.6 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase JAK2 | 5.9 | 5.9 | 5.9 | pKd | 4 |