5L4Q - chain A (model A) | AP2 associated kinase 1
Structure information
PDB: | 5L4Q |
PubMed: | 31136173 |
Release date: | 2016-06-08 |
Resolution: | 1.97 Å |
Kinase: | AAK1 |
Family: | NAK |
Group: | Other |
Species: | HUMAN |
Quality Score: | 9.7 |
Missing Residues: | 0 |
Missing Atoms: | 3 |
DFG conformation: | in |
αC-helix conformation: | in |
Salt bridge KIII.17 and EαC.24: | Yes (2.7Å) |
ASP rotation (xDFG.81) : | 340° |
PHE rotation (xDFG.82) : | 10° |
Activation loop position: | -3.7Å |
αC-helix position: | 18.2Å |
G-rich loop angle: | 52.7° |
G-rich loop distance: | 16Å |
G-rich loop rotation: | 35.3° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I3
H-bond protein
I4
H-bond protein
I5
H-bond ligand
H-bond protein
Binding pocket sequence
Uniprot | EVLAEGGFAIVFLCALKRMVCKREIQIMRDLSKNIVGYIDSLILMDFCRGGQVVNLMNQHQCKTPIIHRDLKVENILLLCDFGSA |
Structure: | EVLAEGGFAIVFLCALKRMVCKREIQIMRDLSKNIVGYIDSLILMDFCRGGQVVNLMNQHQCKTPIIHRDLKVENILLLCDFGSA |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: LKB
Ligand Name: ~{N}-[5-(4-cyanophenyl)-1~{H}-pyrrolo[2,3-b]pyridin-3-yl]pyridine-3-carboxamide
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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 E 50 | 2 V 51 | 3 L 52 | 4 A 53 | 5 E 54 | 6 G 55 | 7 G 56 | 8 F 57 | 9 A 58 | 10 I 59 | 11 V 60 | 12 F 61 | 13 L 62 | 14 C 71 | 15 A 72 | 16 L 73 | 17 K 74 | 18 R 75 | 19 M 76 | 20 V 86 |
■ | ■ | ■ | ■▲ | ||||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 C 87 | 22 K 88 | 23 R 89 | 24 E 90 | 25 I 91 | 26 Q 92 | 27 I 93 | 28 M 94 | 29 R 95 | 30 D 96 | 31 L 97 | 32 S 98 | 33 K 101 | 34 N 102 | 35 I 103 | 36 V 104 | 37 G 105 | 38 Y 106 | 39 I 107 | 40 D 108 |
■ | |||||||||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 S 109 | 42 L 123 | 43 I 124 | 44 L 125 | 45 M 126 | 46 D 127 | 47 F 128 | 48 C 129 | 49 R 130 | 50 G 131 | 51 G 132 | 52 Q 133 | 53 V 134 | 54 V 135 | 55 N 136 | 56 L 137 | 57 M 138 | 58 N 139 | 59 Q 140 | 60 H 166 |
■ | ▲ | ■♦ | ■▲ | ■ | ■ | ■▲ | |||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 Q 167 | 62 C 168 | 63 K 169 | 64 T 170 | 65 P 171 | 66 I 172 | 67 I 173 | 68 H 174 | 69 R 175 | 70 D 176 | 71 L 177 | 72 K 178 | 73 V 179 | 74 E 180 | 75 N 181 | 76 I 182 | 77 L 183 | 78 L 184 | 79 L 192 | 80 C 193 |
■ | ■ | ||||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 194 | 82 F 195 | 83 G 196 | 84 S 197 | 85 A 198 | |||||||||||||||
■ |
Binding affinities
ChEMBL ID:CHEMBL516312Bioaffinities: 19 records for 10 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Adaptor-associated kinase | 5.9 | 5.9 | 5.9 | pIC50 | 1 |
Homo sapiens | Adaptor-associated kinase | 7.3 | 6.9 | 7.3 | pKd | 3 |
Homo sapiens | Adaptor-associated kinase | 6.3 | 6.3 | 6.3 | pKi | 1 |
Homo sapiens | BMP-2-inducible protein kinase | 5 | 5 | 5 | pIC50 | 1 |
Homo sapiens | BMP-2-inducible protein kinase | 5.4 | 5.4 | 5.4 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase 11 | 6.4 | 6.4 | 6.4 | pKd | 2 |
Homo sapiens | Serine/threonine-protein kinase 16 | 4.7 | 4.7 | 4.7 | pIC50 | 1 |
Homo sapiens | Serine/threonine-protein kinase 16 | 7.6 | 7.6 | 7.6 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase 16 | 4.9 | 4.9 | 4.9 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase GAK | 5.5 | 5.5 | 5.5 | pIC50 | 1 |
Homo sapiens | Serine/threonine-protein kinase GAK | 5.8 | 5.8 | 5.8 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase MST2 | 7.1 | 7.1 | 7.1 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase NEK2 | 6.3 | 6.3 | 6.3 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase PIM1 | 7.5 | 7.5 | 7.5 | pKd | 1 |
Homo sapiens | TRAF2- and NCK-interacting kinase | 6.8 | 6.8 | 6.8 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase receptor UFO | 6.2 | 6.2 | 6.2 | pKd | 1 |