4IM3 - chain A (model B) | TANK-binding kinase 1
Structure information
PDB: | 4IM3 |
PubMed: | 23453972 |
Release date: | 2013-03-06 |
Resolution: | 3.34 Å |
Kinase: | TBK1 |
Family: | IKK |
Group: | Other |
Species: | HUMAN |
Quality Score: | 7.7 |
Missing Residues: | 2 |
Missing Atoms: | 11 |
DFG conformation: | in |
αC-helix conformation: | out |
Salt bridge KIII.17 and EαC.24: | No (13.2Å) |
ASP rotation (xDFG.81) : | 346° |
PHE rotation (xDFG.82) : | 354° |
Activation loop position: | -4.3Å |
αC-helix position: | 23.3Å |
G-rich loop angle: | 53.8° |
G-rich loop distance: | 15.9Å |
G-rich loop rotation: | 56.2° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
No waters were found in the defined clusters
Binding pocket sequence
Uniprot | DILGQGATANVFRFAIKVFVQMREFEVLKKLNKNIVKLFAIVLIMEFCPCGSLYTVLEEHLRENGIVHRDIKPGNIMRLTDFGAA |
Structure: | DILGQGATANVFRFAIKVFVQMREFEVLKKLNKNIVKLFAIVLIMEFCPCGSLYTVLEEHLRENGIVHRNIKPGNIMRLTDFG__ |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: BX7
Ligand Name: N-(3-{[5-iodo-4-({3-[(thiophen-2-ylcarbonyl)amino]propyl}amino)pyrimidin-2-yl]amino}phenyl)pyrrolidine-1-carboxamide
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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 D 13 | 2 I 14 | 3 L 15 | 4 G 16 | 5 Q 17 | 6 G 18 | 7 A 19 | 8 T 20 | 9 A 21 | 10 N 22 | 11 V 23 | 12 F 24 | 13 R 25 | 14 F 35 | 15 A 36 | 16 I 37 | 17 K 38 | 18 V 39 | 19 F 40 | 20 V 51 |
■ | ■ | ■ | ■ | ■ | ■ | ||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 Q 52 | 22 M 53 | 23 R 54 | 24 E 55 | 25 F 56 | 26 E 57 | 27 V 58 | 28 L 59 | 29 K 60 | 30 K 61 | 31 L 62 | 32 N 63 | 33 K 65 | 34 N 66 | 35 I 67 | 36 V 68 | 37 K 69 | 38 L 70 | 39 F 71 | 40 A 72 |
■ | |||||||||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 I 73 | 42 V 83 | 43 L 84 | 44 I 85 | 45 M 86 | 46 E 87 | 47 F 88 | 48 C 89 | 49 P 90 | 50 C 91 | 51 G 92 | 52 S 93 | 53 L 94 | 54 Y 95 | 55 T 96 | 56 V 97 | 57 L 98 | 58 E 99 | 59 E 100 | 60 H 125 |
■ | ■ | ■♦ | ■▲▲ | ■ | ■ | ■ | |||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 L 126 | 62 R 127 | 63 E 128 | 64 N 129 | 65 G 130 | 66 I 131 | 67 V 132 | 68 H 133 | 69 R 134 | 70 N 135 | 71 I 136 | 72 K 137 | 73 P 138 | 74 G 139 | 75 N 140 | 76 I 141 | 77 M 142 | 78 R 143 | 79 L 155 | 80 T 156 |
■ | ■ | ||||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 157 | 82 F 158 | 83 G 159 | 84 _ _ | 85 _ _ | |||||||||||||||
■ |
Binding affinities
ChEMBL ID:CHEMBL577784Bioaffinities: 10 records for 5 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Inhibitor of nuclear factor kappa B kinase epsilon subunit | 7.8 | 7.8 | 7.8 | pIC50 | 1 |
Homo sapiens | Pyruvate dehydrogenase kinase isoform 1 | 7.2 | 7.2 | 7.2 | pIC50 | 1 |
Homo sapiens | Serine/threonine-protein kinase TBK1 | 8.1 | 7.4 | 8.2 | pIC50 | 3 |
Homo sapiens | Serine/threonine-protein kinase TBK1 | 7.4 | 6.8 | 7.7 | pKd | 3 |
Homo sapiens | Serine/threonine-protein kinase ULK1 | 7.1 | 7.1 | 7.1 | pIC50 | 1 |
Homo sapiens | Serine/threonine-protein kinase ULK2 | 6.5 | 6.5 | 6.5 | pIC50 | 1 |