6QAT - chain A | Unc-51 like autophagy activating kinase 2
Structure information
PDB: | 6QAT |
PubMed: | 30782972 |
Release date: | 2019-02-27 |
Resolution: | 2.77 Å |
Kinase: | ULK2 |
Family: | ULK |
Group: | Other |
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: | No (4.7Å) |
ASP rotation (xDFG.81) : | 340° |
PHE rotation (xDFG.82) : | 14° |
Activation loop position: | -3.6Å |
αC-helix position: | 17.5Å |
G-rich loop angle: | 57° |
G-rich loop distance: | 16.3Å |
G-rich loop rotation: | 71.1° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond protein
I5
H-bond ligand
H-bond protein
Binding pocket sequence
Uniprot | DLVGHGAFAVVFRVAIKSILLGKEIKILKELQENIVALYDVFLVMEYCNGGDLADYLQAILHSKGIIHRDLKPQNILLIADFGFA |
Structure: | DLVGHGAFAVVFRVAIKSILLGKEIKILKELQENIVALYDVFLVMEYCNGGDLADYLQAILHSKGIIHRDLKPQNILLIADFGFA |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: FE7
Ligand Name: N-{(3Z)-2-oxo-3-[phenyl({4-[(piperidin-1-yl)methyl]phenyl}amino)methylidene]-2,3-dihydro-1H-indol-5-yl}ethanesulfonamide
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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.
- En/disable resizing interacting res.
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 D 13 | 2 L 14 | 3 V 15 | 4 G 16 | 5 H 17 | 6 G 18 | 7 A 19 | 8 F 20 | 9 A 21 | 10 V 22 | 11 V 23 | 12 F 24 | 13 R 25 | 14 V 36 | 15 A 37 | 16 I 38 | 17 K 39 | 18 S 40 | 19 I 41 | 20 L 52 |
■ | ■ | ■ | ■ | ■▲ | |||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 L 53 | 22 G 54 | 23 K 55 | 24 E 56 | 25 I 57 | 26 K 58 | 27 I 59 | 28 L 60 | 29 K 61 | 30 E 62 | 31 L 63 | 32 Q 64 | 33 E 66 | 34 N 67 | 35 I 68 | 36 V 69 | 37 A 70 | 38 L 71 | 39 Y 72 | 40 D 73 |
■ | |||||||||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 V 74 | 42 F 82 | 43 L 83 | 44 V 84 | 45 M 85 | 46 E 86 | 47 Y 87 | 48 C 88 | 49 N 89 | 50 G 90 | 51 G 91 | 52 D 92 | 53 L 93 | 54 A 94 | 55 D 95 | 56 Y 96 | 57 L 97 | 58 Q 98 | 59 A 99 | 60 I 121 |
■ | ▲ | ■♦ | ■▲ | ■ | ■ | ■ | |||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 L 122 | 62 H 123 | 63 S 124 | 64 K 125 | 65 G 126 | 66 I 127 | 67 I 128 | 68 H 129 | 69 R 130 | 70 D 131 | 71 L 132 | 72 K 133 | 73 P 134 | 74 Q 135 | 75 N 136 | 76 I 137 | 77 L 138 | 78 L 139 | 79 I 156 | 80 A 157 |
■ | ■ | ■ | |||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 158 | 82 F 159 | 83 G 160 | 84 F 161 | 85 A 162 | |||||||||||||||
■ |
Binding affinities
ChEMBL ID:CHEMBL514409Bioaffinities: 20 records for 15 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | AMP-activated protein kinase, alpha-1 subunit | 7.7 | 7.7 | 7.7 | pKd | 1 |
Xenopus laevis | Aurora kinase B-A | 8.5 | 8.5 | 8.5 | pIC50 | 1 |
Homo sapiens | BR serine/threonine-protein kinase 2 | 7 | 7 | 7 | pKd | 1 |
Homo sapiens | Focal adhesion kinase 1 | 7.5 | 7.5 | 7.5 | pKd | 1 |
Homo sapiens | Leukocyte tyrosine kinase receptor | 7.3 | 7.3 | 7.3 | pKd | 1 |
Homo sapiens | Maternal embryonic leucine zipper kinase | 6.7 | 6.7 | 6.7 | pIC50 | 1 |
Homo sapiens | Protein tyrosine kinase 2 beta | 8 | 8 | 8 | pKd | 1 |
Homo sapiens | Proto-oncogene tyrosine-protein kinase ROS | 7.1 | 7.1 | 7.1 | pKd | 1 |
Homo sapiens | Ribosomal protein S6 kinase alpha 4 | 7 | 7 | 7 | pKd | 2 |
Homo sapiens | Ribosomal protein S6 kinase alpha 5 | 7.5 | 7.5 | 7.5 | pKd | 2 |
Homo sapiens | Serine/threonine-protein kinase Aurora-A | 8 | 8 | 8 | pIC50 | 1 |
Homo sapiens | Serine/threonine-protein kinase Aurora-B | 6.6 | 6.6 | 8.5 | pIC50 | 3 |
Homo sapiens | Serine/threonine-protein kinase PAK 2 | 4.9 | 4.9 | 4.9 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase FES | 6.8 | 6.8 | 6.8 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase TYK2 | 7.1 | 7.1 | 7.1 | pKd | 2 |