4GIH - chain A (model B) | Tyrosine kinase 2
Structure information
PDB: | 4GIH |
PubMed: | 23867602 |
Release date: | 2013-06-19 |
Resolution: | 2 Å |
Kinase: | TYK2 |
Family: | JakA |
Group: | TK |
Species: | HUMAN |
Quality Score: | 8 |
Missing Residues: | 0 |
Missing Atoms: | 0 |
DFG conformation: | in |
αC-helix conformation: | in |
Salt bridge KIII.17 and EαC.24: | Yes (2.8Å) |
ASP rotation (xDFG.81) : | 355° |
PHE rotation (xDFG.82) : | 16° |
Activation loop position: | -3.7Å |
αC-helix position: | 18.2Å |
G-rich loop angle: | 50° |
G-rich loop distance: | 15Å |
G-rich loop rotation: | 76.9° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond ligand
H-bond protein
I2
H-bond protein
I4
H-bond protein
I9
H-bond ligand
Binding pocket sequence
Uniprot | RDLGEGHFGKVSLVAVKALGWKQEIDILRTLYEHIIKYKGCQLVMEYVPLGSLRDYLPRYLHAQHYIHRDLAARNVLLIGDFGLA |
Structure: | RDLGEGHFGKVSLVAVKALGWKQEIDILRTLYEHIIKYKGCQLVMEYVPLGSLRDYLPRYLHAQHYIHRNLAARNVLLIGDFGLA |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: 0X5
Ligand Name: 2,6-dichloro-N-{2-[(cyclopropylcarbonyl)amino]pyridin-4-yl}benzamide
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- LABELS
- KLIFS residue #
- Amino Acid
- None
- COLORS
- Interaction types
- KLIFS (all res.)
- KLIFS (interacting res.)
- None
- OTHER
- Show/hide non-interacting res.
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This ligand targets the following (sub)pockets:
Main pockets | |
---|---|
Front | |
Gate | |
Back |
Subpockets | |
---|---|
FP-I | |
FP-II | |
BP-I-A | |
BP-I-B | |
BP-II-in | |
BP-II-A-in | |
BP-II-B-in | |
BP-II-out | |
BP-II-B | |
BP-III | |
BP-IV | |
BP-V |
Kinase-ligand interactions
■ 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 R 901 | 2 D 902 | 3 L 903 | 4 G 904 | 5 E 905 | 6 G 906 | 7 H 907 | 8 F 908 | 9 G 909 | 10 K 910 | 11 V 911 | 12 S 912 | 13 L 913 | 14 V 927 | 15 A 928 | 16 V 929 | 17 K 930 | 18 A 931 | 19 L 932 | 20 G 943 |
■ | ■ | ■ | ■ | ■ | ■ | ||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 W 944 | 22 K 945 | 23 Q 946 | 24 E 947 | 25 I 948 | 26 D 949 | 27 I 950 | 28 L 951 | 29 R 952 | 30 T 953 | 31 L 954 | 32 Y 955 | 33 E 957 | 34 H 958 | 35 I 959 | 36 I 960 | 37 K 961 | 38 Y 962 | 39 K 963 | 40 G 964 |
■ | |||||||||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 C 965 | 42 Q 975 | 43 L 976 | 44 V 977 | 45 M 978 | 46 E 979 | 47 Y 980 | 48 V 981 | 49 P 982 | 50 L 983 | 51 G 984 | 52 S 985 | 53 L 986 | 54 R 987 | 55 D 988 | 56 Y 989 | 57 L 990 | 58 P 991 | 59 R 992 | 60 Y 1013 |
■♦ | ■▲▲ | ■ | ■ | ■ | |||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 L 1014 | 62 H 1015 | 63 A 1016 | 64 Q 1017 | 65 H 1018 | 66 Y 1019 | 67 I 1020 | 68 H 1021 | 69 R 1022 | 70 N 1023 | 71 L 1024 | 72 A 1025 | 73 A 1026 | 74 R 1027 | 75 N 1028 | 76 V 1029 | 77 L 1030 | 78 L 1031 | 79 I 1039 | 80 G 1040 |
■ | ■ | ■ | ■ | ||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 1041 | 82 F 1042 | 83 G 1043 | 84 L 1044 | 85 A 1045 | |||||||||||||||
■ |
Binding affinities
ChEMBL ID:CHEMBL2387224Bioaffinities: 33 records for 5 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Cyclin-dependent kinase 9 | 7 | 7 | 7 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase JAK1 | 5.7 | 5.7 | 5.7 | pEC50 | 4 |
Homo sapiens | Tyrosine-protein kinase JAK1 | 7.1 | 7.1 | 7.1 | pKi | 4 |
Homo sapiens | Tyrosine-protein kinase JAK2 | 5.8 | 5.8 | 5.8 | pEC50 | 4 |
Homo sapiens | Tyrosine-protein kinase JAK2 | 7.6 | 7.6 | 7.6 | pKi | 6 |
Homo sapiens | Tyrosine-protein kinase JAK3 | 6.6 | 6.6 | 6.6 | pKi | 4 |
Homo sapiens | Tyrosine-protein kinase TYK2 | 6.4 | 6.4 | 6.4 | pEC50 | 4 |
Homo sapiens | Tyrosine-protein kinase TYK2 | 8.3 | 8.3 | 8.3 | pKi | 6 |