PDB-code
| Kinase structure | |
| Kinase: | CDK1 (CDC2) |
| Family: | CDK |
| Group: | CMGC |
| Species: | HUMAN |
| IUPHAR/BPS ID: | 1961 |
| PDB: | 4Y72 |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2015-08-12 |
| PubMed: | 25864384 |
| Chain: | A |
| (Alternate) Model: | A |
| Orthosteric ligand: | LZ9 |
 | |
| More entries for 4Y72 | |||||
| 4Y72 | Alternative model: | B | Chain: | A | |
| Structural information | |
| DFG conformation: | in |
| αC-helix conformation: | in |
| G-rich loop angle (distance): | 50.1° (15.5Å) |
| G-rich loop rotation: | 61.2° |
| Quality Score: | 8 |
| Resolution: | 2.3 Å |
| Missing Residues: | 0 |
| Missing Atoms: | 0 |
| Ligand binding mode | ||||
| Pockets | Subpockets | Waters | ||
| front | FP-I | Cluster I2 I4 I5 | Ligand No No Yes | Protein Yes Yes Yes |
| Pocket alignment | |
| Uniprot sequence: | EKIGEGTYGVVYKVAMKKITAIREISLLKELRPNIVSLQDVYLIFEFLS-MDLKKYLDSFCHSRRVLHRDLKPQNLLILADFGLA |
| Sequence structure: | EKIGEGTYGVVYKVAMKKITAIREISLLKELRPNIVSLQDVYLIFEFLS_MDLKKYLDSFCHSRRVLHRDLKPQNLLILADFGLA |
| Ligand affinity | |
| ChEMBL ID: | CHEMBL518383 |
| Bioaffinities: | 1 record for 1 kinase |
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | Cyclin-dependent kinase 2 | 8.5 | 8.5 | 8.5 | 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 M 32 | 17 K 33 | 18 K 34 | 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 R 59 | 33 P 61 | 34 N 62 | 35 I 63 | 36 V 64 | 37 S 65 | 38 L 66 | 39 Q 67 | 40 D 68 |
| • | |||||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 V 69 | 42 Y 77 | 43 L 78 | 44 I 79 | 45 F 80 | 46 E 81 | 47 F 82 | 48 L 83 | 49 S 84 | 50 _ _ | 51 M 85 | 52 D 86 | 53 L 87 | 54 K 88 | 55 K 89 | 56 Y 90 | 57 L 91 | 58 D 92 | 59 S 93 | 60 F 118 |
| • | • | •• | ••• | • | • | • | • | ||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 C 119 | 62 H 120 | 63 S 121 | 64 R 122 | 65 R 123 | 66 V 124 | 67 L 125 | 68 H 126 | 69 R 127 | 70 D 128 | 71 L 129 | 72 K 130 | 73 P 131 | 74 Q 132 | 75 N 133 | 76 L 134 | 77 L 135 | 78 I 136 | 79 L 144 | 80 A 145 |
| • | • | ||||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 146 | 82 F 147 | 83 G 148 | 84 L 149 | 85 A 150 | |||||||||||||||
| • | |||||||||||||||||||
Interaction pattern search
Search KLIFS for kinase-ligand complexes with similar interaction patterns:
