PDB-code
| Kinase structure | |
| Kinase: | Pik3cb (p110b) |
| Family: | PIK |
| Group: | Atypical |
| Species: | MOUSE |
| PDB: | 2Y3A |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2011-03-16 |
| PubMed: | 21362552 |
| Chain: | A |
| Orthosteric ligand: | GD9 |
 | |
| Structural information | |
| DFG conformation: | in |
| αC-helix conformation: | in |
| G-rich loop angle (distance): | 62.1° (18.6Å) |
| G-rich loop rotation: | 82.6° |
| Quality Score: | 7.6 |
| Resolution: | 3.3 Å |
| Missing Residues: | 0 |
| Missing Atoms: | 0 |
| Ligand binding mode | ||||
| Pockets | Subpockets | |||
| front gate | BP-I-B | |||
| Pocket alignment | |
| Uniprot sequence: | CKYMDSKMKPLWLVIFKNGDLRQDMLTLQMLRLRMLPYGCLSGLIEVVSSETIADIQLNASYV--LGIGDRHSDNIMVHIDFGHI |
| Sequence structure: | CKYMDSKMKPLWLVIFKNGDLRQDMLTLQMLRLRMLPYGCLSGLIEVVSSETIADIQLNASYV__LGIGDRHSDNIMVHIDFGHI |
| Ligand affinity | |
| ChEMBL ID: | CHEMBL521851 |
| Bioaffinities: | 67 records for 43 kinases |
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | Adaptor-associated kinase | 5 | 5 | 5 | pKd | 1 |
| Homo sapiens | CaM kinase I alpha | 5.3 | 5.3 | 5.3 | pKd | 1 |
| Homo sapiens | CaM kinase I gamma | 5.2 | 5.2 | 5.2 | pKd | 1 |
| Homo sapiens | Casein kinase I delta | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Casein kinase I epsilon | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Casein kinase II alpha (prime) | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | c-Jun N-terminal kinase 1 | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | c-Jun N-terminal kinase 1 | 5.8 | 5.8 | 5.8 | pKi | 1 |
| Homo sapiens | c-Jun N-terminal kinase 2 | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | c-Jun N-terminal kinase 3 | 6.3 | 6.3 | 6.3 | pKd | 1 |
| Homo sapiens | Cyclin-dependent kinase 7 | 5.4 | 5.4 | 5.4 | pKi | 1 |
| Homo sapiens | Death-associated protein kinase 1 | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | Death-associated protein kinase 3 | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | DNA-dependent protein kinase | 5.9 | 5.9 | 5.9 | pIC50 | 1 |
| Homo sapiens | DNA-dependent protein kinase | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Dual specificity protein kinase CLK2 | 6.2 | 6.2 | 6.2 | pKd | 1 |
| Homo sapiens | Dual specificity protein kinase CLK4 | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | Dual specificity protein kinase CLK4 | 6 | 6 | 6 | pKi | 1 |
| Homo sapiens | Dual specificity protein kinase TTK | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | Dual specificity tyrosine-phosphorylation-regulated kinase 1B | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | Dual-specificity tyrosine-phosphorylation regulated kinase 2 | 5.1 | 5.1 | 5.1 | pKd | 1 |
| Homo sapiens | Dual specificty protein kinase CLK1 | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Homeodomain-interacting protein kinase 1 | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Homeodomain-interacting protein kinase 2 | 6.3 | 6.3 | 6.3 | pKd | 1 |
| Homo sapiens | Homeodomain-interacting protein kinase 3 | 6.2 | 6.2 | 6.2 | pKd | 1 |
| Homo sapiens | Homeodomain-interacting protein kinase 4 | 5.3 | 5.3 | 5.3 | pKd | 1 |
| Homo sapiens | Interleukin-1 receptor-associated kinase 3 | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | Leucine-rich repeat serine/threonine-protein kinase 2 | 5.6 | 5.6 | 5.6 | pKi | 1 |
| Homo sapiens | Maternal embryonic leucine zipper kinase | 5.2 | 5.2 | 5.2 | pKd | 1 |
| Homo sapiens | Myosin light chain kinase family member 4 | 6.1 | 6.1 | 6.1 | pKd | 1 |
| Homo sapiens | Nerve growth factor receptor Trk-A | 5.5 | 5.5 | 5.5 | pIC50 | 1 |
| Homo sapiens | Ribosomal protein S6 kinase alpha 3 | 5.5 | 5.5 | 5.5 | pKd | 2 |
| Homo sapiens | Ribosomal protein S6 kinase alpha 6 | 5.3 | 5.3 | 5.3 | pKd | 2 |
| Homo sapiens | Serine/threonine-protein kinase 16 | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase AKT | 7.4 | 7.3 | 7.6 | pIC50 | 3 |
| Homo sapiens | Serine/threonine-protein kinase GAK | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase ICK | 5 | 5 | 5 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase mTOR | 6.4 | 6.2 | 6.9 | pIC50 | 6 |
| Homo sapiens | Serine/threonine-protein kinase mTOR | 6.7 | 6.7 | 7.3 | pKd | 2 |
| Homo sapiens | Serine/threonine-protein kinase mTOR | 6.2 | 6.2 | 6.2 | pKi | 3 |
| Homo sapiens | Serine/threonine-protein kinase PCTAIRE-1 | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase PCTAIRE-3 | 5.3 | 5.3 | 5.3 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase PLK4 | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase RIO2 | 6.2 | 6.2 | 6.2 | pKd | 1 |
| Homo sapiens | SPS1/STE20-related protein kinase YSK4 | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase JAK1 | 6.4 | 6.4 | 6.4 | pKd | 2 |
| Homo sapiens | Tyrosine-protein kinase receptor FLT3 | 5.6 | 5.4 | 6.2 | pKd | 6 |
| Homo sapiens | Tyrosine-protein kinase TYK2 | 5.8 | 5.8 | 5.8 | pKd | 2 |
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 C 770 | 2 K 771 | 3 Y 772 | 4 M 773 | 5 D 774 | 6 S 775 | 7 K 776 | 8 M 777 | 9 K 778 | 10 P 779 | 11 L 780 | 12 W 781 | 13 L 782 | 14 V 796 | 15 I 797 | 16 F 798 | 17 K 799 | 18 N 800 | 19 G 801 | 20 D 803 |
| • | • | •• | • | ||||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 L 804 | 22 R 805 | 23 Q 806 | 24 D 807 | 25 M 808 | 26 L 809 | 27 T 810 | 28 L 811 | 29 Q 812 | 30 M 813 | 31 L 814 | 32 R 815 | 33 L 828 | 34 R 829 | 35 M 830 | 36 L 831 | 37 P 832 | 38 Y 833 | 39 G 834 | 40 C 835 |
| • | ••• | ||||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 L 836 | 42 S 842 | 43 G 843 | 44 L 844 | 45 I 845 | 46 E 846 | 47 V 847 | 48 V 848 | 49 S 849 | 50 S 851 | 51 E 852 | 52 T 853 | 53 I 854 | 54 A 855 | 55 D 856 | 56 I 857 | 57 Q 858 | 58 L 859 | 59 N 860 | 60 A 905 |
| • | • | • | •• | • | |||||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 S 906 | 62 Y 907 | 63 V 908 | 64 _ _ | 65 _ _ | 66 L 909 | 67 G 910 | 68 I 911 | 69 G 912 | 70 D 913 | 71 R 914 | 72 H 915 | 73 S 916 | 74 D 917 | 75 N 918 | 76 I 919 | 77 M 920 | 78 V 921 | 79 H 929 | 80 I 930 |
| • | • | ||||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 931 | 82 F 932 | 83 G 933 | 84 H 934 | 85 I 935 | |||||||||||||||
| • | |||||||||||||||||||
Interaction pattern search
Search KLIFS for kinase-ligand complexes with similar interaction patterns:
