PDB-code
| Kinase structure | |
| Kinase: | CDK2 |
| Family: | CDK |
| Group: | CMGC |
| Species: | HUMAN |
| IUPHAR/BPS ID: | 1973 |
| PDB: | 5MHQ |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2017-12-20 |
| PubMed: | 29063678 |
| Chain: | A |
| (Alternate) Model: | B |
| Orthosteric ligand: | 8QT |
 | |
| More entries for 5MHQ | |||||
| 5MHQ | Alternative model: | A | Chain: | A | |
| Structural information | |
| DFG conformation: | in |
| αC-helix conformation: | out |
| G-rich loop angle (distance): | 49.8° (14.2Å) |
| G-rich loop rotation: | 63.2° |
| Quality Score: | 7.6 |
| Resolution: | 1.3 Å |
| Missing Residues: | 1 |
| Missing Atoms: | 0 |
| Ligand binding mode | ||||
| Pockets | Subpockets | Waters | ||
| front | Cluster I1 I2 I4 I5 | Ligand Yes Yes No No | Protein Yes Yes No Yes | |
| Pocket alignment | |
| Uniprot sequence: | EKIGEGTYGVVYKVALKKITAIREISLLKELNPNIVKLLDVYLVFEFLH-QDLKKFMDAFCHSHRVLHRDLKPQNLLILADFGLA |
| Sequence structure: | EKIGEGTYGVVYKVALK_ITAIREISLLKELNPNIVKLLDVYLVFEFLH_QDLKKFMDAFCHSHRVLHRDLKPQNLLILADFGLA |
| Ligand affinity | |
| ChEMBL ID: | CHEMBL1922219 |
| Bioaffinities: | 7 records for 6 kinases |
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | Cyclin-dependent kinase 1 | 5.7 | 5.7 | 5.7 | pIC50 | 1 |
| Homo sapiens | Cyclin-dependent kinase 2 | 7.5 | 7.5 | 7.5 | pIC50 | 1 |
| Homo sapiens | Cyclin-dependent kinase 4 | 5.2 | 5.2 | 5.2 | pIC50 | 1 |
| Homo sapiens | Cyclin-dependent kinase 7 | 5.9 | 5.9 | 5.9 | pIC50 | 2 |
| Homo sapiens | Cyclin-dependent kinase 9 | 7 | 7 | 7 | pIC50 | 1 |
| Homo sapiens | MAP kinase ERK2 | 4.7 | 4.7 | 4.7 | pIC50 | 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 E 8 | 2 K 9 | 3 I 10 | 4 G 11 | 5 E 12 | 6 G 13 | 7 T 14 | 8 Y 15 | 9 G 16 | 10 V 17 | 11 V 18 | 12 Y 19 | 13 K 20 | 14 V 30 | 15 A 31 | 16 L 32 | 17 K 34 | 18 _ _ | 19 I 35 | 20 T 47 |
| • | • | • | • | • | • | ||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 A 48 | 22 I 49 | 23 R 50 | 24 E 51 | 25 I 52 | 26 S 53 | 27 L 54 | 28 L 55 | 29 K 56 | 30 E 57 | 31 L 58 | 32 N 59 | 33 P 61 | 34 N 62 | 35 I 63 | 36 V 64 | 37 K 65 | 38 L 66 | 39 L 67 | 40 D 68 |
| • | |||||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 V 69 | 42 Y 77 | 43 L 78 | 44 V 79 | 45 F 80 | 46 E 81 | 47 F 82 | 48 L 83 | 49 H 84 | 50 _ _ | 51 Q 85 | 52 D 86 | 53 L 87 | 54 K 88 | 55 K 89 | 56 F 90 | 57 M 91 | 58 D 92 | 59 A 93 | 60 F 117 |
| • | • | •• | ••• | • | • | • | • | ||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 C 118 | 62 H 119 | 63 S 120 | 64 H 121 | 65 R 122 | 66 V 123 | 67 L 124 | 68 H 125 | 69 R 126 | 70 D 127 | 71 L 128 | 72 K 129 | 73 P 130 | 74 Q 131 | 75 N 132 | 76 L 133 | 77 L 134 | 78 I 135 | 79 L 143 | 80 A 144 |
| • | • | • | • | ||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 145 | 82 F 146 | 83 G 147 | 84 L 148 | 85 A 149 | |||||||||||||||
| ••• | |||||||||||||||||||
Interaction pattern search
Search KLIFS for kinase-ligand complexes with similar interaction patterns:
