PDB-code
| Kinase structure | |
| Kinase: | CDC42BPB (MRCKb) |
| Family: | DMPK |
| Group: | AGC |
| Species: | HUMAN |
| IUPHAR/BPS ID: | 1508 |
| PDB: | 3TKU |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2011-10-05 |
| PubMed: | 21949762 |
| Chain: | B |
| Orthosteric ligand: | M77 |
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| More entries for 3TKU | |||
| 3TKU | Chain: | A | |
| Structural information | |
| DFG conformation: | in |
| αC-helix conformation: | in |
| G-rich loop angle (distance): | 47.9° (14.8Å) |
| G-rich loop rotation: | 70.4° |
| Quality Score: | 9.4 |
| Resolution: | 2.15 Å |
| Missing Residues: | 0 |
| Missing Atoms: | 6 |
| Ligand binding mode | ||||
| Pockets | Subpockets | Waters | ||
| front | Cluster I4 I10 | Ligand No No | Protein Yes Yes | |
| Allosteric Ligand | |||||||||||||||||||
| Allosteric ligand: | M77 | ||||||||||||||||||
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| Pocket alignment | |
| Uniprot sequence: | KVIGRGAFGEVAVYAMKILCFREERDVLVNGDQWITALHYAYLVMDYYVGGDLLTLLSKSIHQLHYVHRDIKPDNVLLLADFGSC |
| Sequence structure: | KVIGRGAFGEVAVYAMKILCFREERDVLVNGDQWITALHYAYLVMDYYVGGDLLTLLSKSIHQLHYVHRDIKPDNVLLLADFGSC |
| Ligand affinity | |
| ChEMBL ID: | CHEMBL38380 |
| Bioaffinities: | 76 records for 29 kinases |
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | cAMP-dependent protein kinase alpha-catalytic subunit | 7.1 | 7.1 | 7.1 | pKi | 2 |
| Homo sapiens | Cell division protein kinase 8 | 5.9 | 5.9 | 5.9 | pKi | 2 |
| Homo sapiens | Cyclin-dependent kinase 5 | 5.6 | 5.6 | 5.6 | pKi | 2 |
| Homo sapiens | Cyclin-dependent kinase 7 | 5.6 | 5.6 | 5.6 | pKi | 2 |
| Homo sapiens | Death-associated protein kinase 3 | 5.9 | 5.9 | 5.9 | pKi | 2 |
| Homo sapiens | Dual specificity protein kinase CLK4 | 6.5 | 6.5 | 6.5 | pKi | 2 |
| Homo sapiens | Leucine-rich repeat serine/threonine-protein kinase 2 | 5.7 | 5.7 | 5.7 | pKi | 2 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 4 | 5.6 | 5.6 | 5.6 | pKi | 2 |
| Homo sapiens | Myosin light chain kinase, smooth muscle | 4.7 | 4.7 | 5.4 | pIC50 | 2 |
| Homo sapiens | Myosin light chain kinase, smooth muscle | 4.4 | 4.4 | 4.4 | pKi | 1 |
| Homo sapiens | Protein kinase C delta | 5.6 | 5.6 | 5.6 | pKi | 2 |
| Homo sapiens | Protein kinase C epsilon | 5.5 | 5.5 | 5.5 | pIC50 | 2 |
| Homo sapiens | Protein kinase C gamma | 5.4 | 5.4 | 5.4 | pKi | 2 |
| Homo sapiens | Protein kinase C nu | 6 | 6 | 6 | pKi | 2 |
| Homo sapiens | Protein kinase C theta | 6.2 | 6.2 | 6.2 | pKi | 2 |
| Homo sapiens | Protein kinase N1 | 5.8 | 5.8 | 5.8 | pIC50 | 1 |
| Homo sapiens | Protein kinase N2 | 6.1 | 5.4 | 6.1 | pIC50 | 3 |
| Homo sapiens | Rho-associated protein kinase 1 | 6.2 | 5.4 | 6.6 | pIC50 | 6 |
| Homo sapiens | Rho-associated protein kinase 1 | 6.3 | 6.3 | 7.5 | pKi | 6 |
| Homo sapiens | Rho-associated protein kinase 2 | 6.2 | 4.9 | 6.8 | pIC50 | 8 |
| Homo sapiens | Rho-associated protein kinase 2 | 7.1 | 7.1 | 7.1 | pKd | 1 |
| Homo sapiens | Rho-associated protein kinase 2 | 7.3 | 7.3 | 7.3 | pKi | 2 |
| Rattus norvegicus | Rho-associated protein kinase 2 | 5.7 | 5.7 | 5.7 | pIC50 | 1 |
| Homo sapiens | Ribosomal protein S6 kinase 1 | 6 | 6 | 6 | pKi | 1 |
| Homo sapiens | Ribosomal protein S6 kinase alpha 3 | 6 | 6 | 6 | pKi | 4 |
| Homo sapiens | Ribosomal protein S6 kinase alpha 5 | 5.3 | 5.3 | 5.3 | pIC50 | 2 |
| Homo sapiens | Serine/threonine-protein kinase AKT | 5.5 | 5.5 | 5.5 | pKi | 2 |
| Homo sapiens | Serine/threonine-protein kinase AKT3 | 5.2 | 5.2 | 5.2 | pKi | 2 |
| Homo sapiens | Serine/threonine-protein kinase Aurora-B | 5.6 | 5.6 | 5.6 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase Chk2 | 5.1 | 5.1 | 5.1 | pKi | 2 |
| Homo sapiens | Serine/threonine-protein kinase D2 | 5.9 | 5.9 | 5.9 | pKi | 2 |
| Homo sapiens | Serine/threonine-protein kinase PRKX | 7.3 | 7.3 | 7.3 | pKi | 2 |
| Homo sapiens | Serine/threonine-protein kinase Sgk2 | 5.2 | 5.2 | 5.2 | pKi | 1 |
Kinase-ligand interaction pattern
• 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 80 | 2 V 81 | 3 I 82 | 4 G 83 | 5 R 84 | 6 G 85 | 7 A 86 | 8 F 87 | 9 G 88 | 10 E 89 | 11 V 90 | 12 A 91 | 13 V 92 | 14 Y 102 | 15 A 103 | 16 M 104 | 17 K 105 | 18 I 106 | 19 L 107 | 20 C 120 |
| • | • | • | • | • | • | ||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 F 121 | 22 R 122 | 23 E 123 | 24 E 124 | 25 R 125 | 26 D 126 | 27 V 127 | 28 L 128 | 29 V 129 | 30 N 130 | 31 G 131 | 32 D 132 | 33 Q 134 | 34 W 135 | 35 I 136 | 36 T 137 | 37 A 138 | 38 L 139 | 39 H 140 | 40 Y 141 |
| • | |||||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 A 142 | 42 Y 150 | 43 L 151 | 44 V 152 | 45 M 153 | 46 D 154 | 47 Y 155 | 48 Y 156 | 49 V 157 | 50 G 158 | 51 G 159 | 52 D 160 | 53 L 161 | 54 L 162 | 55 T 163 | 56 L 164 | 57 L 165 | 58 S 166 | 59 K 167 | 60 S 190 |
| • | • | •• | ••• | ||||||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 I 191 | 62 H 192 | 63 Q 193 | 64 L 194 | 65 H 195 | 66 Y 196 | 67 V 197 | 68 H 198 | 69 R 199 | 70 D 200 | 71 I 201 | 72 K 202 | 73 P 203 | 74 D 204 | 75 N 205 | 76 V 206 | 77 L 207 | 78 L 208 | 79 L 216 | 80 A 217 |
| • | • | • | • | ||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 218 | 82 F 219 | 83 G 220 | 84 S 221 | 85 C 222 | |||||||||||||||
Interaction pattern search
Search KLIFS for kinase-ligand complexes with similar interaction patterns:
