4WNP - chain A (model B) | Unc-51 like autophagy activating kinase 1
Structure information
PDB: | 4WNP |
PubMed: | 25551253 |
Release date: | 2015-01-14 |
Resolution: | 1.88 Å |
Kinase: | ULK1 |
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: | Yes (2.5Å) |
ASP rotation (xDFG.81) : | 347° |
PHE rotation (xDFG.82) : | 19° |
Activation loop position: | -3.7Å |
αC-helix position: | 17.5Å |
G-rich loop angle: | 52.6° |
G-rich loop distance: | 15.7Å |
G-rich loop rotation: | 38.1° |
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
I5
H-bond protein
I11
H-bond ligand
H-bond protein
Binding pocket sequence
Uniprot | DLIGHGAFAVVFKVAVKCILLGKEIKILKELKENIVALYDFYLVMEYCNGGDLADYLHALLHSKGIIHRDLKPQNILLIADFGFA |
Structure: | DLIGHGAFAVVFKVAVKCILLGKEIKILKELKENIVALYDFYLVMEYCNGGDLADYLHALLHSKGIIHRDLKPQNILLIADFGFA |
Modified residues
Residue 180 (not in pocket)
Phosphorylated threonine
Orthosteric ligand
Ligand HET-code: 3RJ
Ligand Name: N~2~-(1H-benzimidazol-6-yl)-N~4~-(5-cyclobutyl-1H-pyrazol-3-yl)quinazoline-2,4-diamine
- Download image
- 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 20 | 2 L 21 | 3 I 22 | 4 G 23 | 5 H 24 | 6 G 25 | 7 A 26 | 8 F 27 | 9 A 28 | 10 V 29 | 11 V 30 | 12 F 31 | 13 K 32 | 14 V 43 | 15 A 44 | 16 V 45 | 17 K 46 | 18 C 47 | 19 I 48 | 20 L 59 |
■ | ■ | ■ | ■ | ||||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 L 60 | 22 G 61 | 23 K 62 | 24 E 63 | 25 I 64 | 26 K 65 | 27 I 66 | 28 L 67 | 29 K 68 | 30 E 69 | 31 L 70 | 32 K 71 | 33 E 73 | 34 N 74 | 35 I 75 | 36 V 76 | 37 A 77 | 38 L 78 | 39 Y 79 | 40 D 80 |
■ | |||||||||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 F 81 | 42 Y 89 | 43 L 90 | 44 V 91 | 45 M 92 | 46 E 93 | 47 Y 94 | 48 C 95 | 49 N 96 | 50 G 97 | 51 G 98 | 52 D 99 | 53 L 100 | 54 A 101 | 55 D 102 | 56 Y 103 | 57 L 104 | 58 H 105 | 59 A 106 | 60 L 128 |
■ | ▲ | ■♦ | ■▲▲ | ■ | ■ | ||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 L 129 | 62 H 130 | 63 S 131 | 64 K 132 | 65 G 133 | 66 I 134 | 67 I 135 | 68 H 136 | 69 R 137 | 70 D 138 | 71 L 139 | 72 K 140 | 73 P 141 | 74 Q 142 | 75 N 143 | 76 I 144 | 77 L 145 | 78 L 146 | 79 I 163 | 80 A 164 |
▲ | ■ | ■ | ■ | ||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 165 | 82 F 166 | 83 G 167 | 84 F 168 | 85 A 169 | |||||||||||||||
■ |
Binding affinities
ChEMBL ID:CHEMBL3605055Bioaffinities: 4 records for 3 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Pyruvate dehydrogenase kinase isoform 1 | 6.4 | 6.4 | 6.4 | pIC50 | 1 |
Homo sapiens | Serine/threonine-protein kinase ULK1 | 8.1 | 8.1 | 8.3 | pIC50 | 2 |
Homo sapiens | Serine/threonine-protein kinase ULK2 | 7.9 | 7.9 | 7.9 | pIC50 | 1 |