PDB-code
| Kinase structure | |
| Kinase: | PLK2 |
| Family: | PLK |
| Group: | Other |
| Species: | HUMAN |
| IUPHAR/BPS ID: | 2169 |
| PDB: | 4I5M |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2013-12-25 |
| PubMed: | 23794260 |
| Chain: | A |
| Orthosteric ligand: | R78 |
 | |
| Structural information | |
| DFG conformation: | in |
| αC-helix conformation: | in |
| G-rich loop angle (distance): | 59° (16.9Å) |
| G-rich loop rotation: | 71.2° |
| Quality Score: | 8 |
| Resolution: | 1.8 Å |
| Missing Residues: | 0 |
| Missing Atoms: | 0 |
| Ligand binding mode | ||||
| Pockets | Subpockets | Waters | ||
| front | BP-I-A BP-I-B | Cluster I2 I4 I5 I10 | Ligand No No Yes Yes | Protein No Yes Yes Yes |
| Pocket alignment | |
| Uniprot sequence: | KVLGKGGFAKCYEYAAKIIKIDKEIELHRILHKHVVQFYHYYILLEYCSRRSMAHILKAYLHEQEILHRDLKLGNFFIVGDFGLA |
| Sequence structure: | KTLGKGGFAKCYEYAAKIIKIDKEIELHRILHKHVVQFYHYYILLEYCSRRSMAHILKAYLHEQEILHRDLKLGNFFIVGDFGLA |
| Ligand affinity | |
| ChEMBL ID: | CHEMBL513909 |
| Bioaffinities: | 112 records for 78 kinases |
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | Adaptor-associated kinase | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | ALK tyrosine kinase receptor | 6.8 | 6.8 | 6.8 | pKd | 1 |
| Homo sapiens | CaM kinase I delta | 5.3 | 5.3 | 5.3 | pKd | 1 |
| Homo sapiens | CaM kinase II alpha | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | CaM kinase II beta | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | CaM kinase II delta | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | CaM kinase II gamma | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | CaM-kinase kinase alpha | 7.7 | 7.7 | 7.7 | pKd | 1 |
| Homo sapiens | CaM-kinase kinase beta | 7.6 | 7.6 | 7.6 | pKd | 1 |
| Homo sapiens | Casein kinase I alpha | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Casein kinase I delta | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | Casein kinase I epsilon | 6.4 | 6.4 | 6.4 | pKd | 1 |
| Homo sapiens | Casein kinase I gamma 1 | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | Casein kinase I gamma 2 | 5.2 | 5.2 | 5.2 | pKd | 1 |
| Homo sapiens | Casein kinase I isoform gamma-3 | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Citron Rho-interacting kinase | 5.3 | 5.3 | 5.3 | pKd | 1 |
| Homo sapiens | c-Jun N-terminal kinase 3 | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Cyclin-dependent kinase 4 | 5.7 | 5.7 | 5.7 | pKd | 1 |
| Homo sapiens | Cyclin-dependent kinase 7 | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Death-associated protein kinase 1 | 6.3 | 6.3 | 6.3 | pKd | 1 |
| Homo sapiens | Death-associated protein kinase 2 | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Death-associated protein kinase 3 | 6.9 | 6.9 | 6.9 | pKd | 1 |
| Homo sapiens | Dual specificity protein kinase CLK2 | 6.3 | 6.3 | 6.3 | pKd | 1 |
| Homo sapiens | Dual specificity protein kinase CLK3 | 6.2 | 6.2 | 6.2 | pKd | 1 |
| Homo sapiens | Dual specificity protein kinase TTK | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Dual specificty protein kinase CLK1 | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Epidermal growth factor receptor erbB1 | 5.7 | 5.2 | 6.6 | pKd | 12 |
| Homo sapiens | Focal adhesion kinase 1 | 6.8 | 6.8 | 6.8 | pKd | 1 |
| Homo sapiens | G protein-coupled receptor kinase 7 | 6.1 | 6.1 | 6.1 | pKd | 1 |
| Homo sapiens | Hepatocyte growth factor receptor | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Homeodomain-interacting protein kinase 1 | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | Homeodomain-interacting protein kinase 2 | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Homeodomain-interacting protein kinase 3 | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | Homeodomain-interacting protein kinase 4 | 5.7 | 5.7 | 5.7 | pKd | 1 |
| Homo sapiens | Hormonally up-regulated neu tumor-associated kinase | 5 | 5 | 5 | pKd | 1 |
| Homo sapiens | Interferon-induced, double-stranded RNA-activated protein kinase | 6.3 | 6.3 | 6.3 | pKd | 1 |
| Homo sapiens | Interleukin-1 receptor-associated kinase 1 | 5.7 | 5.7 | 5.7 | pKd | 1 |
| Homo sapiens | Interleukin-1 receptor-associated kinase 4 | 5.7 | 5.7 | 5.7 | pKd | 1 |
| Homo sapiens | Leukocyte tyrosine kinase receptor | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Misshapen-like kinase 1 | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | Mitogen-activated protein kinase 7 | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Myosin IIIA | 5.2 | 5.2 | 5.2 | pKd | 1 |
| Homo sapiens | Myosin-IIIB | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Myosin light chain kinase, smooth muscle | 7 | 7 | 7 | pKd | 1 |
| Homo sapiens | Myotonin-protein kinase | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Phosphorylase kinase gamma subunit 2 | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | Protein kinase C mu | 6.5 | 6.5 | 6.5 | pKd | 1 |
| Homo sapiens | Protein kinase C nu | 6.5 | 6.5 | 6.5 | pKd | 1 |
| Homo sapiens | Protein tyrosine kinase 2 beta | 6.5 | 6.5 | 6.5 | pKd | 1 |
| Homo sapiens | Proto-oncogene tyrosine-protein kinase MER | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Ribosomal protein S6 kinase alpha 1 | 5.3 | 5.3 | 5.3 | pKd | 2 |
| Homo sapiens | Ribosomal protein S6 kinase alpha 2 | 6.2 | 6.2 | 6.2 | pKd | 2 |
| Homo sapiens | Ribosomal protein S6 kinase alpha 4 | 7.9 | 7.9 | 7.9 | pKd | 2 |
| Homo sapiens | Ribosomal protein S6 kinase alpha 5 | 6.6 | 6.6 | 6.6 | pKd | 2 |
| Homo sapiens | Ribosomal protein S6 kinase alpha 6 | 5.9 | 5.9 | 5.9 | pKd | 2 |
| Homo sapiens | Serine/threonine-protein kinase 10 | 5.3 | 5.3 | 5.3 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase 16 | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase 2 | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase 33 | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase Chk2 | 5.1 | 5.1 | 5.1 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase D2 | 6.3 | 6.3 | 6.3 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase DCLK1 | 5.2 | 5.2 | 5.2 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase GAK | 6.8 | 6.8 | 6.8 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase NEK2 | 5.7 | 5.7 | 5.7 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase Nek3 | 6.1 | 6.1 | 6.1 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase NEK7 | 5.2 | 5.2 | 5.2 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase NIM1 | 6.1 | 6.1 | 6.1 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase PLK1 | 9.1 | 8.1 | 9.1 | pIC50 | 8 |
| Homo sapiens | Serine/threonine-protein kinase PLK1 | 9.7 | 9.7 | 9.7 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase PLK1 | 8.5 | 8.5 | 9.7 | pKi | 2 |
| Homo sapiens | Serine/threonine-protein kinase PLK2 | 7.5 | 7.5 | 7.9 | pIC50 | 2 |
| Homo sapiens | Serine/threonine-protein kinase PLK2 | 9.1 | 9.1 | 9.1 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase PLK3 | 7.1 | 7.1 | 7.7 | pIC50 | 2 |
| Homo sapiens | Serine/threonine-protein kinase PLK3 | 8.4 | 8.4 | 8.4 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase RIO1 | 5.7 | 5.7 | 5.7 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase RIO3 | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase TAO3 | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | SPS1/STE20-related protein kinase YSK4 | 6.3 | 6.3 | 6.3 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase ABL | 5.6 | 5.2 | 5.7 | pKd | 5 |
| Homo sapiens | Tyrosine-protein kinase FES | 5.7 | 5.7 | 5.7 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase receptor FLT3 | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase SYK | 5.3 | 5.3 | 5.3 | pKd | 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 K 57 | 2 T 58 | 3 L 59 | 4 G 60 | 5 K 61 | 6 G 62 | 7 G 63 | 8 F 64 | 9 A 65 | 10 K 66 | 11 C 67 | 12 Y 68 | 13 E 69 | 14 Y 79 | 15 A 80 | 16 A 81 | 17 K 82 | 18 I 83 | 19 I 84 | 20 K 97 |
| • | • | •• | • | • | • | • | • | • | • | ||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 I 98 | 22 D 99 | 23 K 100 | 24 E 101 | 25 I 102 | 26 E 103 | 27 L 104 | 28 H 105 | 29 R 106 | 30 I 107 | 31 L 108 | 32 H 109 | 33 K 111 | 34 H 112 | 35 V 113 | 36 V 114 | 37 Q 115 | 38 F 116 | 39 Y 117 | 40 H 118 |
| • | |||||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 Y 119 | 42 Y 127 | 43 I 128 | 44 L 129 | 45 L 130 | 46 E 131 | 47 Y 132 | 48 C 133 | 49 S 134 | 50 R 135 | 51 R 136 | 52 S 137 | 53 M 138 | 54 A 139 | 55 H 140 | 56 I 141 | 57 L 142 | 58 K 143 | 59 A 144 | 60 Y 166 |
| • | • | • | ••• | • | • | ||||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 L 167 | 62 H 168 | 63 E 169 | 64 Q 170 | 65 E 171 | 66 I 172 | 67 L 173 | 68 H 174 | 69 R 175 | 70 D 176 | 71 L 177 | 72 K 178 | 73 L 179 | 74 G 180 | 75 N 181 | 76 F 182 | 77 F 183 | 78 I 184 | 79 V 192 | 80 G 193 |
| •• | |||||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 194 | 82 F 195 | 83 G 196 | 84 L 197 | 85 A 198 | |||||||||||||||
Interaction pattern search
Search KLIFS for kinase-ligand complexes with similar interaction patterns:
