PDB-code
| Kinase structure | |
| Kinase: | NEK2 |
| Family: | NEK |
| Group: | Other |
| Species: | HUMAN |
| IUPHAR/BPS ID: | 2117 |
| PDB: | 4AFE |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2012-04-25 |
| PubMed: | 22404346 |
| Chain: | A |
| Orthosteric ligand: | GGY |
 | |
| Structural information | |
| DFG conformation: | out |
| αC-helix conformation: | out |
| G-rich loop angle (distance): | 65.8° (20.1Å) |
| G-rich loop rotation: | 55.9° |
| Quality Score: | 5.6 |
| Resolution: | 2.6 Å |
| Missing Residues: | 8 |
| Missing Atoms: | 12 |
| Ligand binding mode | ||||
| Pockets | Subpockets | Waters | ||
| front | Cluster I2 | Ligand No | Protein Yes | |
| Pocket alignment | |
| Uniprot sequence: | YTIGTGSYGRCQKLVWKELMLVSEVNLLRELKPNIVRYYDRYIVMEYCEGGDLASVITKSDGGHTVLHRDLKPANVFLLGDFGLA |
| Sequence structure: | YTIGTGSYGRCQKLVWKELMLVSEVNLLRELKPNIVRYYDRYIVMEYCEGGDLASVITKS_______HRDLKPANVFLLGDFGL_ |
| Ligand affinity | |
| ChEMBL ID: | CHEMBL2042135 |
| Bioaffinities: | 15 records for 14 kinases |
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | Cyclin-dependent kinase 2 | 5.3 | 5.3 | 5.3 | pIC50 | 1 |
| Homo sapiens | Dual specificity protein kinase TTK | 5.1 | 5.1 | 5.1 | pIC50 | 1 |
| Homo sapiens | Glycogen synthase kinase-3 beta | 7.2 | 7.2 | 7.2 | pIC50 | 1 |
| Homo sapiens | Hepatocyte growth factor receptor | 5.9 | 5.9 | 5.9 | pIC50 | 1 |
| Homo sapiens | Serine/threonine-protein kinase Aurora-A | 5.3 | 5.3 | 5.3 | pIC50 | 1 |
| Homo sapiens | Serine/threonine-protein kinase Chk2 | 5.7 | 5.7 | 5.7 | pIC50 | 1 |
| Homo sapiens | Serine/threonine-protein kinase D2 | 6.5 | 6.5 | 6.5 | pIC50 | 1 |
| Homo sapiens | Serine/threonine-protein kinase NEK2 | 6.1 | 6.1 | 7.7 | pIC50 | 2 |
| Homo sapiens | Serine/threonine-protein kinase PLK1 | 5.2 | 5.2 | 5.2 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase ABL | 6 | 6 | 6 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase FYN | 6.1 | 6.1 | 6.1 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase LCK | 7 | 7 | 7 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase Lyn | 5.9 | 5.9 | 5.9 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase SRC | 6.1 | 6.1 | 6.1 | 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 Y 12 | 2 T 13 | 3 I 14 | 4 G 15 | 5 T 16 | 6 G 17 | 7 S 18 | 8 Y 19 | 9 G 20 | 10 R 21 | 11 C 22 | 12 Q 23 | 13 K 24 | 14 L 34 | 15 V 35 | 16 W 36 | 17 K 37 | 18 E 38 | 19 L 39 | 20 M 51 |
| • | • | • | • | • | • | ||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 L 52 | 22 V 53 | 23 S 54 | 24 E 55 | 25 V 56 | 26 N 57 | 27 L 58 | 28 L 59 | 29 R 60 | 30 E 61 | 31 L 62 | 32 K 63 | 33 P 65 | 34 N 66 | 35 I 67 | 36 V 68 | 37 R 69 | 38 Y 70 | 39 Y 71 | 40 D 72 |
| • | |||||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 R 73 | 42 Y 83 | 43 I 84 | 44 V 85 | 45 M 86 | 46 E 87 | 47 Y 88 | 48 C 89 | 49 E 90 | 50 G 91 | 51 G 92 | 52 D 93 | 53 L 94 | 54 A 95 | 55 S 96 | 56 V 97 | 57 I 98 | 58 T 99 | 59 K 100 | 60 S 131 |
| • | • | ••• | •• | • | • | ||||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 _ _ | 62 _ _ | 63 _ _ | 64 _ _ | 65 _ _ | 66 _ _ | 67 _ _ | 68 H 139 | 69 R 140 | 70 D 141 | 71 L 142 | 72 K 143 | 73 P 144 | 74 A 145 | 75 N 146 | 76 V 147 | 77 F 148 | 78 L 149 | 79 L 157 | 80 G 158 |
| ••• | • | ||||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 159 | 82 F 160 | 83 G 161 | 84 L 162 | 85 _ _ | |||||||||||||||
| ••• | • | ||||||||||||||||||
Interaction pattern search
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