PDB-code
| Kinase structure | |
| Kinase: | CDK12 (CRK7) |
| Family: | CDK |
| Group: | CMGC |
| Species: | HUMAN |
| PDB: | 8BU9 |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2023-09-13 |
| PubMed: | 37679459 |
| Chain: | B |
| Orthosteric ligand: | RRC |
 | |
| Structural information | |
| DFG conformation: | in |
| αC-helix conformation: | in |
| G-rich loop angle (distance): | 56.9° (16.8Å) |
| G-rich loop rotation: | 78.9° |
| Quality Score: | 8 |
| Resolution: | 3.51 Å |
| Missing Residues: | 0 |
| Missing Atoms: | 0 |
| Ligand binding mode | ||||
| Pockets | Subpockets | |||
| front | ||||
| Pocket alignment | |
| Uniprot sequence: | GIIGEGTYGQVYKVALKKVTAIREIKILRQLIRSVVNMKEIYLVFEYMD-HDLMGLLESYCHKKNFLHRDIKCSNILLLADFGLA |
| Sequence structure: | GIIGEGTYGQVYKVALKKVTAIREIKILRQLIRSVVNMKEIYLVFEYMD_HDLMGLLESYCHKKNFLHRDIKCSNILLLADFGLA |
| 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 G 731 | 2 I 732 | 3 I 733 | 4 G 734 | 5 E 735 | 6 G 736 | 7 T 737 | 8 Y 738 | 9 G 739 | 10 Q 740 | 11 V 741 | 12 Y 742 | 13 K 743 | 14 V 753 | 15 A 754 | 16 L 755 | 17 K 756 | 18 K 757 | 19 V 758 | 20 T 770 |
| • | • | • | • | ||||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 A 771 | 22 I 772 | 23 R 773 | 24 E 774 | 25 I 775 | 26 K 776 | 27 I 777 | 28 L 778 | 29 R 779 | 30 Q 780 | 31 L 781 | 32 I 782 | 33 R 784 | 34 S 785 | 35 V 786 | 36 V 787 | 37 N 788 | 38 M 789 | 39 K 790 | 40 E 791 |
| • | |||||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 I 792 | 42 Y 810 | 43 L 811 | 44 V 812 | 45 F 813 | 46 E 814 | 47 Y 815 | 48 M 816 | 49 D 817 | 50 _ _ | 51 H 818 | 52 D 819 | 53 L 820 | 54 M 821 | 55 G 822 | 56 L 823 | 57 L 824 | 58 E 825 | 59 S 826 | 60 Y 849 |
| • | • | • | •• | • | • | • | |||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 C 850 | 62 H 851 | 63 K 852 | 64 K 853 | 65 N 854 | 66 F 855 | 67 L 856 | 68 H 857 | 69 R 858 | 70 D 859 | 71 I 860 | 72 K 861 | 73 C 862 | 74 S 863 | 75 N 864 | 76 I 865 | 77 L 866 | 78 L 867 | 79 L 875 | 80 A 876 |
| • | • | ||||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 877 | 82 F 878 | 83 G 879 | 84 L 880 | 85 A 881 | |||||||||||||||
Interaction pattern search
Search KLIFS for kinase-ligand complexes with similar interaction patterns:
