5WNI - chain A | Receptor-interacting serine-threonine kinase 4
Structure information
PDB: | 5WNI |
PubMed: | 29706531 |
Release date: | 2018-05-09 |
Resolution: | 2.65 Å |
Kinase: | Ripk4 (ANKRD3) |
Family: | RIPK |
Group: | TKL |
Species: | MOUSE |
Quality Score: | 7.1 |
Missing Residues: | 4 |
Missing Atoms: | 13 |
DFG conformation: | in |
αC-helix conformation: | in |
Salt bridge KIII.17 and EαC.24: | Yes (2.5Å) |
ASP rotation (xDFG.81) : | 340° |
PHE rotation (xDFG.82) : | 8° |
Activation loop position: | -3.3Å |
αC-helix position: | 17.1Å |
G-rich loop angle: | - |
G-rich loop distance: | - |
G-rich loop rotation: | - |
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond ligand
H-bond protein
Binding pocket sequence
Uniprot | EKVGSGGFGQVYKLAIKCSELLEEAKKMEMAKRYILPVYGIGLVMEYMETGSLEKLLASHCMSPPLLHLDLKPANILLISDFGLA |
Structure: | EKVGS____QVYKLAIKCSELLEEAKKMEMAKRYILPVYGIGLVMEYMETGSLEKLLASHCMSPPLLHLNLKPANILLISDFGLA |
Modified residues
No modified residues identified.
Orthosteric ligand
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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 26 | 2 K 27 | 3 V 28 | 4 G 29 | 5 S 30 | 6 _ _ | 7 _ _ | 8 _ _ | 9 _ _ | 10 Q 35 | 11 V 36 | 12 Y 37 | 13 K 38 | 14 L 48 | 15 A 49 | 16 I 50 | 17 K 51 | 18 C 52 | 19 S 53 | 20 E 65 |
■ | ■ | ■ | ▲● | ||||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 L 66 | 22 L 67 | 23 E 68 | 24 E 69 | 25 A 70 | 26 K 71 | 27 K 72 | 28 M 73 | 29 E 74 | 30 M 75 | 31 A 76 | 32 K 77 | 33 R 79 | 34 Y 80 | 35 I 81 | 36 L 82 | 37 P 83 | 38 V 84 | 39 Y 85 | 40 G 86 |
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 I 87 | 42 G 93 | 43 L 94 | 44 V 95 | 45 M 96 | 46 E 97 | 47 Y 98 | 48 M 99 | 49 E 100 | 50 T 101 | 51 G 102 | 52 S 103 | 53 L 104 | 54 E 105 | 55 K 106 | 56 L 107 | 57 L 108 | 58 A 109 | 59 S 110 | 60 H 133 |
■ | ▲ | ■♦ | ■▲ | ■ | |||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 C 134 | 62 M 135 | 63 S 136 | 64 P 137 | 65 P 138 | 66 L 139 | 67 L 140 | 68 H 141 | 69 L 142 | 70 N 143 | 71 L 144 | 72 K 145 | 73 P 146 | 74 A 147 | 75 N 148 | 76 I 149 | 77 L 150 | 78 L 151 | 79 I 159 | 80 S 160 |
▲ | ■ | ||||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 161 | 82 F 162 | 83 G 163 | 84 L 164 | 85 A 165 | |||||||||||||||
Binding affinities
ChEMBL ID:CHEMBL14249Bioaffinities: 8 records for 3 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | MAP kinase-activated protein kinase 2 | 5.2 | 4.9 | 5.6 | pIC50 | 3 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase 7 | 5.6 | 5.6 | 5.6 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase JAK2 | 5.9 | 5.9 | 5.9 | pKd | 4 |