PDB-code
| Kinase structure | |
| Kinase: | CDK6 |
| Family: | CDK |
| Group: | CMGC |
| Species: | HUMAN |
| IUPHAR/BPS ID: | 1978 |
| PDB: | 5L2I |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2016-08-24 |
| PubMed: | 27496135 |
| Chain: | A |
| Orthosteric ligand: | LQQ |
 | |
| Structural information | |
| DFG conformation: | in |
| αC-helix conformation: | out |
| G-rich loop angle (distance): | 50.4° (15.3Å) |
| G-rich loop rotation: | 52.8° |
| Quality Score: | 9.3 |
| Resolution: | 2.75 Å |
| Missing Residues: | 1 |
| Missing Atoms: | 3 |
| Ligand binding mode | ||||
| Pockets | Subpockets | |||
| front | ||||
| Pocket alignment | |
| Uniprot sequence: | AEIGEGAYGKVFKVALKRVSTIREVAVLRHLEPNVVRLFDVTLVFEHVD-QDLTTYLDKFLHSHRVVHRDLKPQNILVLADFGLA |
| Sequence structure: | AEIGEGAYGKVFKVALKRVSTIREVAVLRHLEPNVVRLFDVTLVFEHVD_QDLTTYLDKFLHSHRVVHRDLKPQNILVLADFGL_ |
| Ligand affinity | |
| ChEMBL ID: | CHEMBL189963 |
| Bioaffinities: | 46 records for 31 kinases |
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | ALK tyrosine kinase receptor | 5.8 | 5.8 | 5.8 | pKi | 1 |
| Homo sapiens | AMP-activated protein kinase, alpha-1 subunit | 6 | 6 | 6 | pKi | 1 |
| Homo sapiens | c-Jun N-terminal kinase 1 | 5.8 | 5.8 | 5.8 | pKi | 1 |
| Homo sapiens | c-Jun N-terminal kinase 2 | 5.4 | 5.4 | 5.4 | pKi | 1 |
| Homo sapiens | Cyclin-dependent kinase 2 | 8 | 8 | 8 | pIC50 | 1 |
| Homo sapiens | Cyclin-dependent kinase 4 | 8 | 7.8 | 8 | pIC50 | 5 |
| Homo sapiens | Cyclin-dependent kinase 5 | 6.5 | 6.5 | 6.5 | pKi | 2 |
| Homo sapiens | Cyclin-dependent kinase 6 | 7.8 | 7.7 | 7.8 | pIC50 | 3 |
| Homo sapiens | Cyclin-dependent kinase 9 | 6.1 | 6.1 | 6.1 | pIC50 | 2 |
| Homo sapiens | Cyclin-dependent kinase 9 | 6.4 | 6.4 | 6.4 | pKi | 1 |
| Homo sapiens | Death-associated protein kinase 3 | 6.9 | 6.9 | 6.9 | pKi | 2 |
| Homo sapiens | Dual specificity protein kinase CLK2 | 6.5 | 6.5 | 6.5 | pKi | 1 |
| Homo sapiens | Dual specificity protein kinase CLK4 | 7.7 | 7.7 | 7.7 | pKi | 2 |
| Homo sapiens | Dual-specificity tyrosine-phosphorylation regulated kinase 1A | 6.1 | 6.1 | 6.1 | pKi | 1 |
| Homo sapiens | Dual specificity tyrosine-phosphorylation-regulated kinase 1B | 7 | 7 | 7 | pKi | 2 |
| Homo sapiens | Hepatocyte growth factor receptor | 5.6 | 5.6 | 5.6 | pKi | 1 |
| Homo sapiens | Leucine-rich repeat serine/threonine-protein kinase 2 | 5.6 | 5.6 | 5.6 | pKi | 1 |
| Homo sapiens | Macrophage-stimulating protein receptor | 5.5 | 5.5 | 5.5 | pKi | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 2 | 5.6 | 5.6 | 5.6 | pKi | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 4 | 5.9 | 5.9 | 5.9 | pKi | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 5 | 5.8 | 5.8 | 5.8 | pKi | 1 |
| Homo sapiens | Protein kinase C nu | 6.4 | 6.4 | 6.4 | pKi | 1 |
| Homo sapiens | Rho-associated protein kinase 2 | 6.9 | 6.9 | 6.9 | pKi | 2 |
| Homo sapiens | Ribosomal protein S6 kinase alpha 3 | 6.1 | 6.1 | 6.1 | pKi | 2 |
| Homo sapiens | Serine/threonine-protein kinase Chk1 | 5.6 | 5.6 | 5.6 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase NEK2 | 5.5 | 5.5 | 5.5 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase PAK 4 | 5.4 | 5.4 | 5.4 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase PRKX | 5.6 | 5.6 | 5.6 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase TAO1 | 6.3 | 6.3 | 6.3 | pKi | 1 |
| Homo sapiens | Tyrosine-protein kinase JAK3 | 7.2 | 7.2 | 7.2 | pIC50 | 2 |
| Homo sapiens | Tyrosine-protein kinase receptor FLT3 | 5.5 | 5.5 | 5.5 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase receptor RET | 5.6 | 5.6 | 5.6 | 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 A 17 | 2 E 18 | 3 I 19 | 4 G 20 | 5 E 21 | 6 G 22 | 7 A 23 | 8 Y 24 | 9 G 25 | 10 K 26 | 11 V 27 | 12 F 28 | 13 K 29 | 14 V 40 | 15 A 41 | 16 L 42 | 17 K 43 | 18 R 44 | 19 V 45 | 20 S 57 |
| • | • | • | • | ||||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 T 58 | 22 I 59 | 23 R 60 | 24 E 61 | 25 V 62 | 26 A 63 | 27 V 64 | 28 L 65 | 29 R 66 | 30 H 67 | 31 L 68 | 32 E 69 | 33 P 74 | 34 N 75 | 35 V 76 | 36 V 77 | 37 R 78 | 38 L 79 | 39 F 80 | 40 D 81 |
| • | |||||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 V 82 | 42 T 95 | 43 L 96 | 44 V 97 | 45 F 98 | 46 E 99 | 47 H 100 | 48 V 101 | 49 D 102 | 50 _ _ | 51 Q 103 | 52 D 104 | 53 L 105 | 54 T 106 | 55 T 107 | 56 Y 108 | 57 L 109 | 58 D 110 | 59 K 111 | 60 F 135 |
| • | • | •• | • | • | • | ||||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 L 136 | 62 H 137 | 63 S 138 | 64 H 139 | 65 R 140 | 66 V 141 | 67 V 142 | 68 H 143 | 69 R 144 | 70 D 145 | 71 L 146 | 72 K 147 | 73 P 148 | 74 Q 149 | 75 N 150 | 76 I 151 | 77 L 152 | 78 V 153 | 79 L 161 | 80 A 162 |
| • | • | • | • | ||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 163 | 82 F 164 | 83 G 165 | 84 L 166 | 85 _ _ | |||||||||||||||
| •• | |||||||||||||||||||
Interaction pattern search
Search KLIFS for kinase-ligand complexes with similar interaction patterns:
