5VUB - chain B (model A) | Pim-1 proto-oncogene, serine/threonine kinase
Structure information
PDB: | 5VUB |
PubMed: | 29111719 |
Release date: | 2017-12-13 |
Resolution: | 2 Å |
Kinase: | PIM1 |
Family: | PIM |
Group: | CAMK |
Species: | HUMAN |
Quality Score: | 7.6 |
Missing Residues: | 1 |
Missing Atoms: | 0 |
DFG conformation: | in |
αC-helix conformation: | in |
Salt bridge KIII.17 and EαC.24: | Yes (2.4Å) |
ASP rotation (xDFG.81) : | 341° |
PHE rotation (xDFG.82) : | 7° |
Activation loop position: | -3.9Å |
αC-helix position: | 17.9Å |
G-rich loop angle: | 57.4° |
G-rich loop distance: | 17.7Å |
G-rich loop rotation: | 45.2° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond protein
I4
H-bond protein
I5
H-bond ligand
H-bond protein
I7
No H-bonds
Binding pocket sequence
Uniprot | PLLGSGGFGSVYSVAIKHVRVPMEVVLLKKVSSGVIRLLDWVLILERPEVQDLFDFITEHCHNCGVLHRDIKDENILILIDFGSG |
Structure: | PLLGSGGFGSVYSVAIKHVRVPMEVVLLKKVSSGVIRLLDWVLILERPEVQDLFDFITEHCHN_GVLHRDIKDENILILIDFGSG |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: 8GU
Ligand Name: (2Z)-6-methoxy-7-(piperazin-1-ylmethyl)-2-(1H-pyrrolo[3,2-b]pyridin-3-ylmethylidene)-1-benzofuran-3-one
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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 P 42 | 2 L 43 | 3 L 44 | 4 G 45 | 5 S 46 | 6 G 47 | 7 G 48 | 8 F 49 | 9 G 50 | 10 S 51 | 11 V 52 | 12 Y 53 | 13 S 54 | 14 V 64 | 15 A 65 | 16 I 66 | 17 K 67 | 18 H 68 | 19 V 69 | 20 R 85 |
■ | ■ | ■ | ■♦ | ■ | ■ | ■▲ | |||||||||||||
αC | b.l | IV | |||||||||||||||||
21 V 86 | 22 P 87 | 23 M 88 | 24 E 89 | 25 V 90 | 26 V 91 | 27 L 92 | 28 L 93 | 29 K 94 | 30 K 95 | 31 V 96 | 32 S 97 | 33 S 101 | 34 G 102 | 35 V 103 | 36 I 104 | 37 R 105 | 38 L 106 | 39 L 107 | 40 D 108 |
■ | |||||||||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 W 109 | 42 V 117 | 43 L 118 | 44 I 119 | 45 L 120 | 46 E 121 | 47 R 122 | 48 P 123 | 49 E 124 | 50 V 126 | 51 Q 127 | 52 D 128 | 53 L 129 | 54 F 130 | 55 D 131 | 56 F 132 | 57 I 133 | 58 T 134 | 59 E 135 | 60 H 157 |
■ | ▲ | ■ | ■ | ■ | ■▲● | ||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 C 158 | 62 H 159 | 63 N 160 | 64 _ _ | 65 G 162 | 66 V 163 | 67 L 164 | 68 H 165 | 69 R 166 | 70 D 167 | 71 I 168 | 72 K 169 | 73 D 170 | 74 E 171 | 75 N 172 | 76 I 173 | 77 L 174 | 78 I 175 | 79 L 184 | 80 I 185 |
■ | ■ | ||||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 186 | 82 F 187 | 83 G 188 | 84 S 189 | 85 G 190 | |||||||||||||||
■ |
Binding affinities
ChEMBL ID:CHEMBL2147770Bioaffinities: 2 records for 1 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Serine/threonine-protein kinase PIM1 | 6.4 | 6.4 | 6.4 | pIC50 | 2 |