PDB-code
| Kinase structure | |
| Kinase: | NEK1 |
| Family: | NEK |
| Group: | Other |
| Species: | HUMAN |
| IUPHAR/BPS ID: | 2114 |
| PDB: | 4B9D |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2012-09-19 |
| PubMed: | 28710492 |
| Chain: | B |
| (Alternate) Model: | B |
| Orthosteric ligand: | CK7 |
 | |
| More entries for 4B9D | |||||
| 4B9D | Alternative model: | A | Chain: | A | |
| 4B9D | Alternative model: | A | Chain: | B | |
| 4B9D | Alternative model: | B | Chain: | A | |
| Structural information | |
| DFG conformation: | out-like |
| αC-helix conformation: | out |
| G-rich loop angle (distance): | - |
| G-rich loop rotation: | - |
| Quality Score: | 6.7 |
| Resolution: | 1.9 Å |
| Missing Residues: | 5 |
| Missing Atoms: | 13 |
| Ligand binding mode | ||||
| Pockets | Subpockets | Waters | ||
| front | Cluster I2 I5 | Ligand No No | Protein Yes Yes | |
| Pocket alignment | |
| Uniprot sequence: | QKIGEGSFGKAILYVIKEIESRREVAVLANMKPNIVQYRESYIVMDYCEGGDLFKRINAHVHDRKILHRDIKSQNIFLLGDFGIA |
| Sequence structure: | QKIG_____KAILYVIKEIESRREVAVLANMKPNIVQYRESYIVMDYCEGGDLFKRINAHVHDRKILHRDIKSQNIFLLGDFGIA |
| Ligand affinity | |
| ChEMBL ID: | CHEMBL298445 |
| Bioaffinities: | 13 records for 9 kinases |
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | Cyclin-dependent kinase 1 | 7.1 | 7.1 | 7.1 | pKi | 1 |
| Homo sapiens | Cyclin-dependent kinase 2 | 8.7 | 8.7 | 8.7 | pKi | 3 |
| Homo sapiens | Cyclin-dependent kinase 4 | 7.3 | 7.3 | 7.3 | pKi | 2 |
| Homo sapiens | Cyclin-dependent kinase 7 | 7.2 | 7.2 | 7.2 | pKi | 1 |
| Homo sapiens | Cyclin-dependent kinase 9 | 8.4 | 8.4 | 8.4 | pKi | 1 |
| Homo sapiens | Glycogen synthase kinase-3 beta | 7.7 | 7.7 | 7.7 | pKi | 2 |
| Homo sapiens | Serine/threonine-protein kinase Aurora-A | 7.1 | 7.1 | 7.1 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase Aurora-B | 7.2 | 7.2 | 7.2 | pKi | 1 |
| Homo sapiens | Tyrosine-protein kinase ABL | 6.8 | 6.8 | 6.8 | 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 Q 8 | 2 K 9 | 3 I 10 | 4 G 11 | 5 _ _ | 6 _ _ | 7 _ _ | 8 _ _ | 9 _ _ | 10 K 17 | 11 A 18 | 12 I 19 | 13 L 20 | 14 Y 30 | 15 V 31 | 16 I 32 | 17 K 33 | 18 E 34 | 19 I 35 | 20 E 47 |
| • | • | • | • | ||||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 S 48 | 22 R 49 | 23 R 50 | 24 E 51 | 25 V 52 | 26 A 53 | 27 V 54 | 28 L 55 | 29 A 56 | 30 N 57 | 31 M 58 | 32 K 59 | 33 P 61 | 34 N 62 | 35 I 63 | 36 V 64 | 37 Q 65 | 38 Y 66 | 39 R 67 | 40 E 68 |
| • | |||||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 S 69 | 42 Y 77 | 43 I 78 | 44 V 79 | 45 M 80 | 46 D 81 | 47 Y 82 | 48 C 83 | 49 E 84 | 50 G 85 | 51 G 86 | 52 D 87 | 53 L 88 | 54 F 89 | 55 K 90 | 56 R 91 | 57 I 92 | 58 N 93 | 59 A 94 | 60 H 118 |
| • | • | •• | ••• | • | |||||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 V 119 | 62 H 120 | 63 D 121 | 64 R 122 | 65 K 123 | 66 I 124 | 67 L 125 | 68 H 126 | 69 R 127 | 70 D 128 | 71 I 129 | 72 K 130 | 73 S 131 | 74 Q 132 | 75 N 133 | 76 I 134 | 77 F 135 | 78 L 136 | 79 L 144 | 80 G 145 |
| ••• | |||||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 146 | 82 F 147 | 83 G 148 | 84 I 149 | 85 A 150 | |||||||||||||||
Interaction pattern search
Search KLIFS for kinase-ligand complexes with similar interaction patterns:
