5DH3 - chain A (model A) | Serine/threonine kinase 3
Structure information
PDB: | 5DH3 |
PubMed: | 27535619 |
Release date: | 2016-08-31 |
Resolution: | 2.47 Å |
Kinase: | STK3 (MST2) |
Family: | STE20 |
Group: | STE |
Species: | HUMAN |
Quality Score: | 9.6 |
Missing Residues: | 0 |
Missing Atoms: | 4 |
DFG conformation: | in |
αC-helix conformation: | in |
Salt bridge KIII.17 and EαC.24: | Yes (3.9Å) |
ASP rotation (xDFG.81) : | 343° |
PHE rotation (xDFG.82) : | 1° |
Activation loop position: | -3.2Å |
αC-helix position: | 18Å |
G-rich loop angle: | 54.9° |
G-rich loop distance: | 15.3Å |
G-rich loop rotation: | 84.8° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I10
H-bond ligand
Binding pocket sequence
Uniprot | EKLGEGSYGSVFKVAIKQVEIIKEISIMQQCDPYVVKYYGSWIVMEYCGAGSVSDIIRLYLHFMRKIHRDIKAGNILLLADFGVA |
Structure: | EKLGEGSYGSVFKVAIKQVEIIKEISIMQQCDPYVVKYYGSWIVMEYCGAGSVSDIIRLYLHFMRKIHRDIKAGNILLLADFGVA |
Modified residues
Residue 174 (not in pocket)
Phosphorylated threonine
Residue 180 (not in pocket)
Phosphorylated threonine
Orthosteric ligand
Ligand HET-code: 5BS
Ligand Name: 4-[(5,10-dimethyl-6-oxo-6,10-dihydro-5H-pyrimido[5,4-b]thieno[3,2-e][1,4]diazepin-2-yl)amino]benzenesulfonamide
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- LABELS
- KLIFS residue #
- Amino Acid
- None
- COLORS
- Interaction types
- KLIFS (all res.)
- KLIFS (interacting res.)
- None
- OTHER
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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 E 31 | 2 K 32 | 3 L 33 | 4 G 34 | 5 E 35 | 6 G 36 | 7 S 37 | 8 Y 38 | 9 G 39 | 10 S 40 | 11 V 41 | 12 F 42 | 13 K 43 | 14 V 53 | 15 A 54 | 16 I 55 | 17 K 56 | 18 Q 57 | 19 V 58 | 20 E 66 |
■ | ■ | ■ | ■ | ||||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 I 67 | 22 I 68 | 23 K 69 | 24 E 70 | 25 I 71 | 26 S 72 | 27 I 73 | 28 M 74 | 29 Q 75 | 30 Q 76 | 31 C 77 | 32 D 78 | 33 P 80 | 34 Y 81 | 35 V 82 | 36 V 83 | 37 K 84 | 38 Y 85 | 39 Y 86 | 40 G 87 |
■ | |||||||||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 S 88 | 42 W 96 | 43 I 97 | 44 V 98 | 45 M 99 | 46 E 100 | 47 Y 101 | 48 C 102 | 49 G 103 | 50 A 104 | 51 G 105 | 52 S 106 | 53 V 107 | 54 S 108 | 55 D 109 | 56 I 110 | 57 I 111 | 58 R 112 | 59 L 113 | 60 Y 136 |
■ | ■ | ■♦ | ■▲▲ | ■ | ■ | ■ | ▲ | ||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 L 137 | 62 H 138 | 63 F 139 | 64 M 140 | 65 R 141 | 66 K 142 | 67 I 143 | 68 H 144 | 69 R 145 | 70 D 146 | 71 I 147 | 72 K 148 | 73 A 149 | 74 G 150 | 75 N 151 | 76 I 152 | 77 L 153 | 78 L 154 | 79 L 162 | 80 A 163 |
■ | ■ | ||||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 164 | 82 F 165 | 83 G 166 | 84 V 167 | 85 A 168 | |||||||||||||||
■ |
Binding affinities
ChEMBL ID:CHEMBL4554938Bioaffinities: No (p)Ki/(p)IC50/(p)EC50 values for kinases found (with a ChEMBL confidence ≥ 8).