PDB-code
| Kinase structure | |
| Kinase: | Pik3cd (p110d) |
| Family: | PIK |
| Group: | Atypical |
| Species: | MOUSE |
| PDB: | 7R26 |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2022-05-18 |
| PubMed: | 35500094 |
| Chain: | A |
| Orthosteric ligand: | SD5 |
 | |
| Structural information | |
| DFG conformation: | in |
| αC-helix conformation: | in |
| G-rich loop angle (distance): | 62.1° (18.8Å) |
| G-rich loop rotation: | 82.9° |
| Quality Score: | 8.7 |
| Resolution: | 2.3 Å |
| Missing Residues: | 1 |
| Missing Atoms: | 9 |
| Ligand binding mode | ||||
| Pockets | Subpockets | Waters | ||
| front gate back | BP-I-A | Cluster I7 I10 | Ligand No No | Protein Yes Yes |
| Pocket alignment | |
| Uniprot sequence: | CTFMDSKMKPLWIIIFKNGDLRQDMLTLQMIQLRMTPYGCLTGLIEVVLSDTIANIQLNATYV--LGIGDRHSDNIMIHIDFGHF |
| Sequence structure: | CTFMDSKMKPLWIIIFKNGDLRQDMLTLQMIQLRMTPYGCLTGLIEVVLSDTIANIQL_ATYV__LGIGDRHSDNIMIHIDFGHF |
| Ligand affinity | |
| ChEMBL ID: | CHEMBL2017974 |
| Bioaffinities: | 7 records for 2 kinases |
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | DNA-dependent protein kinase | 5.2 | 5.2 | 5.2 | pIC50 | 1 |
| Homo sapiens | DNA-dependent protein kinase | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase mTOR | 5.7 | 5.3 | 7 | pIC50 | 3 |
| Homo sapiens | Serine/threonine-protein kinase mTOR | 7.7 | 7.7 | 7.7 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase mTOR | 6.7 | 6.7 | 6.7 | 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 C 749 | 2 T 750 | 3 F 751 | 4 M 752 | 5 D 753 | 6 S 754 | 7 K 755 | 8 M 756 | 9 K 757 | 10 P 758 | 11 L 759 | 12 W 760 | 13 I 761 | 14 I 776 | 15 I 777 | 16 F 778 | 17 K 779 | 18 N 780 | 19 G 781 | 20 D 783 |
| • | • | • | • | • | |||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 L 784 | 22 R 785 | 23 Q 786 | 24 D 787 | 25 M 788 | 26 L 789 | 27 T 790 | 28 L 791 | 29 Q 792 | 30 M 793 | 31 I 794 | 32 Q 795 | 33 L 808 | 34 R 809 | 35 M 810 | 36 T 811 | 37 P 812 | 38 Y 813 | 39 G 814 | 40 C 815 |
| • | •• | • | |||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 L 816 | 42 T 822 | 43 G 823 | 44 L 824 | 45 I 825 | 46 E 826 | 47 V 827 | 48 V 828 | 49 L 829 | 50 S 831 | 51 D 832 | 52 T 833 | 53 I 834 | 54 A 835 | 55 N 836 | 56 I 837 | 57 Q 838 | 58 L 839 | 59 _ _ | 60 A 885 |
| • | • | • | •• | • | |||||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 T 886 | 62 Y 887 | 63 V 888 | 64 _ _ | 65 _ _ | 66 L 889 | 67 G 890 | 68 I 891 | 69 G 892 | 70 D 893 | 71 R 894 | 72 H 895 | 73 S 896 | 74 D 897 | 75 N 898 | 76 I 899 | 77 M 900 | 78 I 901 | 79 H 909 | 80 I 910 |
| • | • | ||||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 911 | 82 F 912 | 83 G 913 | 84 H 914 | 85 F 915 | |||||||||||||||
| • | |||||||||||||||||||
Interaction pattern search
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