PDB-code
| Kinase structure | |
| Kinase: | CDK2 |
| Family: | CDK |
| Group: | CMGC |
| Species: | HUMAN |
| IUPHAR/BPS ID: | 1973 |
| PDB: | 3DDQ |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2008-07-22 |
| PubMed: | 18574471 |
| Chain: | A |
| (Alternate) Model: | A |
| Orthosteric ligand: | RRC |
 | |
| More entries for 3DDQ | |||||
| 3DDQ | Alternative model: | A | Chain: | C | |
| 3DDQ | Alternative model: | B | Chain: | A | |
| 3DDQ | Alternative model: | B | Chain: | C | |
| Structural information | |
| DFG conformation: | in |
| αC-helix conformation: | in |
| G-rich loop angle (distance): | 51.7° (15.2Å) |
| G-rich loop rotation: | 71.9° |
| Quality Score: | 8 |
| Resolution: | 1.8 Å |
| Missing Residues: | 0 |
| Missing Atoms: | 0 |
| Ligand binding mode | ||||
| Pockets | Subpockets | Waters | ||
| front | FP-I | Cluster I1 I2 I5 I9 I10 I11 | Ligand No No No Yes No Yes | Protein Yes Yes Yes Yes No Yes |
| Pocket alignment | |
| Uniprot sequence: | EKIGEGTYGVVYKVALKKITAIREISLLKELNPNIVKLLDVYLVFEFLH-QDLKKFMDAFCHSHRVLHRDLKPQNLLILADFGLA |
| Sequence structure: | EKIGEGTYGVVYKVALKKITAIREISLLKELNPNIVKLLDVYLVFEFLH_QDLKKFMDAFCHSHRVLHRDLKPQNLLILADFGLA |
| Ligand affinity | |
| ChEMBL ID: | CHEMBL14762 |
| Bioaffinities: | 62 records for 29 kinases |
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | ALK tyrosine kinase receptor | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Casein kinase I alpha | 5.4 | 5.4 | 5.4 | pIC50 | 1 |
| Homo sapiens | Casein kinase I delta | 6.6 | 6.6 | 6.6 | pKd | 1 |
| Homo sapiens | Casein kinase I epsilon | 6.5 | 6.5 | 6.8 | pKd | 2 |
| Homo sapiens | Casein kinase I gamma 1 | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Casein kinase I gamma 2 | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Casein kinase I isoform gamma-3 | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Cyclin-dependent kinase 1 | 6.4 | 5.6 | 6.7 | pIC50 | 6 |
| Homo sapiens | Cyclin-dependent kinase 2 | 6.2 | 6.2 | 7 | pIC50 | 8 |
| Homo sapiens | Cyclin-dependent kinase 2 | 5.5 | 5.5 | 5.5 | pKd | 2 |
| Homo sapiens | Cyclin-dependent kinase 4 | 4 | 4 | 4 | pIC50 | 1 |
| Homo sapiens | Cyclin-dependent kinase 5 | 6.8 | 6 | 6.8 | pIC50 | 4 |
| Homo sapiens | Cyclin-dependent kinase 5 | 5.7 | 5.7 | 5.7 | pKd | 2 |
| Homo sapiens | Cyclin-dependent kinase 7 | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Mus musculus | Dual specificity protein kinase CLK1 | 5.4 | 5.4 | 5.9 | pIC50 | 2 |
| Homo sapiens | Dual specificity protein kinase CLK2 | 6.2 | 6.2 | 6.3 | pKd | 2 |
| Mus musculus | Dual specificity protein kinase CLK2 | 6.2 | 6.2 | 6.2 | pIC50 | 1 |
| Homo sapiens | Dual specificity protein kinase CLK4 | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Mus musculus | Dual specificity protein kinase CLK4 | 6.2 | 6.2 | 6.2 | pIC50 | 1 |
| Homo sapiens | Dual specificity protein kinase TTK | 5.7 | 5.7 | 5.8 | pKd | 2 |
| Rattus norvegicus | Dual specificity tyrosine-phosphorylation-regulated kinase 1A | 5 | 5 | 5 | pIC50 | 1 |
| Homo sapiens | Dual-specificity tyrosine-phosphorylation regulated kinase 1A | 5.5 | 4.8 | 5.9 | pIC50 | 6 |
| Mus musculus | Dual-specificity tyrosine-phosphorylation regulated kinase 1A | 5.3 | 5.3 | 5.3 | pIC50 | 1 |
| Homo sapiens | Dual specificity tyrosine-phosphorylation-regulated kinase 1B | 5.9 | 5.9 | 5.9 | pIC50 | 1 |
| Homo sapiens | Dual specificity tyrosine-phosphorylation-regulated kinase 1B | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Dual-specificity tyrosine-phosphorylation regulated kinase 2 | 5.8 | 5.8 | 5.8 | pIC50 | 1 |
| Homo sapiens | Dual specificty protein kinase CLK1 | 5.7 | 5.7 | 5.9 | pKd | 2 |
| Homo sapiens | MAP kinase ERK1 | 4.5 | 4.5 | 4.5 | pIC50 | 2 |
| Homo sapiens | MAP kinase ERK2 | 4.9 | 4.9 | 4.9 | pIC50 | 2 |
| Homo sapiens | Ribosomal protein S6 kinase alpha 2 | 5.5 | 5.5 | 5.5 | pKd | 2 |
| Homo sapiens | Serine/threonine-protein kinase PAK 4 | 5.2 | 5.2 | 5.2 | pIC50 | 1 |
| Homo sapiens | Serine/threonine-protein kinase PCTAIRE-1 | 6 | 6 | 6 | 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 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 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 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
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