4QMM - chain A | Serine/threonine kinase 24
Structure information
PDB: | 4QMM |
PubMed: | 27135311 |
Release date: | 2015-07-01 |
Resolution: | 1.85 Å |
Kinase: | STK24 (MST3) |
Family: | STE20 |
Group: | STE |
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 (2.7Å) |
ASP rotation (xDFG.81) : | 352° |
PHE rotation (xDFG.82) : | 12° |
Activation loop position: | -3.3Å |
αC-helix position: | 17.8Å |
G-rich loop angle: | 54.2° |
G-rich loop distance: | 15.7Å |
G-rich loop rotation: | 76° |
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I2
H-bond protein
I3
H-bond protein
I4
H-bond protein
I5
H-bond protein
I10
H-bond ligand
H-bond protein
Binding pocket sequence
Uniprot | EKIGKGSFGEVFKVAIKIIDIQQEITVLSQCDPYVTKYYGSWIIMEYLGGGSALDLLEPYLHSEKKIHRDIKAANVLLLADFGVA |
Structure: | EKIGKGSFGEVFKVAIKIIDIQQEITVLSQCDPYVTKYYGSWIIMEYLGGGSALDLLEPYLHSEKKIHRDIKAANVLLLADFGVA |
Modified residues
Residue 178 (not in pocket)
Phosphorylated threonine
Orthosteric ligand
Ligand HET-code: 35R
Ligand Name: 1-cyclopropyl-3-{3-[5-(morpholin-4-ylmethyl)-1H-benzimidazol-2-yl]-1H-pyrazol-4-yl}urea
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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 28 | 2 K 29 | 3 I 30 | 4 G 31 | 5 K 32 | 6 G 33 | 7 S 34 | 8 F 35 | 9 G 36 | 10 E 37 | 11 V 38 | 12 F 39 | 13 K 40 | 14 V 50 | 15 A 51 | 16 I 52 | 17 K 53 | 18 I 54 | 19 I 55 | 20 D 66 |
■ | ■ | ■ | ■ | ■ | |||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 I 67 | 22 Q 68 | 23 Q 69 | 24 E 70 | 25 I 71 | 26 T 72 | 27 V 73 | 28 L 74 | 29 S 75 | 30 Q 76 | 31 C 77 | 32 D 78 | 33 P 80 | 34 Y 81 | 35 V 82 | 36 T 83 | 37 K 84 | 38 Y 85 | 39 Y 86 | 40 G 87 |
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 S 88 | 42 W 96 | 43 I 97 | 44 I 98 | 45 M 99 | 46 E 100 | 47 Y 101 | 48 L 102 | 49 G 103 | 50 G 104 | 51 G 105 | 52 S 106 | 53 A 107 | 54 L 108 | 55 D 109 | 56 L 110 | 57 L 111 | 58 E 112 | 59 P 113 | 60 Y 134 |
▲ | ■♦ | ■▲▲ | ■ | ■ | ■ | ||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 L 135 | 62 H 136 | 63 S 137 | 64 E 138 | 65 K 139 | 66 K 140 | 67 I 141 | 68 H 142 | 69 R 143 | 70 D 144 | 71 I 145 | 72 K 146 | 73 A 147 | 74 A 148 | 75 N 149 | 76 V 150 | 77 L 151 | 78 L 152 | 79 L 160 | 80 A 161 |
■ | |||||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 162 | 82 F 163 | 83 G 164 | 84 V 165 | 85 A 166 | |||||||||||||||
Binding affinities
ChEMBL ID:CHEMBL495727Bioaffinities: 166 records for 123 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Activin receptor type-1 | 7.1 | 7.1 | 7.1 | pKd | 1 |
Homo sapiens | Activin receptor type-1B | 6.1 | 6.1 | 6.1 | pKd | 1 |
Homo sapiens | Adaptor-associated kinase | 7.8 | 7.8 | 7.8 | pKd | 1 |
Homo sapiens | AMP-activated protein kinase, alpha-1 subunit | 7.3 | 7.3 | 7.3 | pKd | 1 |
Homo sapiens | AMP-activated protein kinase, gamma-1 subunit | 7.5 | 7.5 | 7.5 | pKd | 1 |
Homo sapiens | AMP-activated protein kinase, gamma-2 subunit | 7.2 | 7.2 | 7.2 | pKd | 1 |
Homo sapiens | BMP-2-inducible protein kinase | 7.5 | 7.5 | 7.5 | pKd | 1 |
Homo sapiens | Bone morphogenetic protein receptor type-1A | 6.4 | 6.4 | 6.4 | pKd | 1 |
Homo sapiens | Bone morphogenetic protein receptor type-1B | 7.7 | 7.7 | 7.7 | pKd | 1 |
Homo sapiens | Bone morphogenetic protein receptor type-2 | 7.4 | 7.4 | 7.4 | pKd | 1 |
Homo sapiens | Breakpoint cluster region protein | 6.8 | 6.8 | 6.8 | pKd | 2 |
Homo sapiens | cAMP-dependent protein kinase alpha-catalytic subunit | 5.5 | 5.5 | 5.5 | pKd | 1 |
Homo sapiens | cAMP-dependent protein kinase beta-1 catalytic subunit | 6 | 6 | 6 | pKd | 1 |
Homo sapiens | cAMP-dependent protein kinase, gamma catalytic subunit | 8.5 | 8.5 | 8.5 | pKd | 1 |
Homo sapiens | Casein kinase II alpha (prime) | 7.2 | 7.2 | 7.2 | pKd | 1 |
Homo sapiens | Cell division cycle 7-related protein kinase | 6.3 | 6.3 | 6.3 | pKd | 1 |
Homo sapiens | c-Jun N-terminal kinase 1 | 6.8 | 6.8 | 6.8 | pKd | 1 |
Homo sapiens | c-Jun N-terminal kinase 2 | 6.3 | 6.3 | 6.3 | pKd | 1 |
Homo sapiens | c-Jun N-terminal kinase 3 | 6.5 | 6.5 | 6.5 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 10 | 8.1 | 8.1 | 8.1 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 4 | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 5 | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 6 | 6.9 | 6.9 | 6.9 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 9 | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Dual specificity mitogen-activated protein kinase kinase 5 | 7.3 | 7.3 | 7.3 | pKd | 1 |
Homo sapiens | Dual specificity mitogen-activated protein kinase kinase 6 | 5.5 | 5.5 | 5.5 | pKd | 1 |
Homo sapiens | Dual-specificity tyrosine-phosphorylation regulated kinase 1A | 5.6 | 5.6 | 5.6 | pKd | 1 |
Homo sapiens | Dual specificty protein kinase CLK1 | 5.7 | 5.7 | 5.7 | pKd | 1 |
Homo sapiens | Ephrin type-A receptor 2 | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Ephrin type-A receptor 4 | 4.4 | 4.4 | 4.4 | pKd | 1 |
Homo sapiens | Ephrin type-A receptor 7 | 8.1 | 8.1 | 8.1 | pKd | 1 |
Homo sapiens | Ephrin type-B receptor 6 | 7.9 | 7.9 | 7.9 | pKd | 1 |
Homo sapiens | Fibroblast growth factor receptor 1 | 8 | 8 | 8 | pIC50 | 2 |
Homo sapiens | Fibroblast growth factor receptor 1 | 7.6 | 7.6 | 7.6 | pKd | 1 |
Homo sapiens | Fibroblast growth factor receptor 2 | 8 | 8 | 9 | pIC50 | 2 |
Homo sapiens | Fibroblast growth factor receptor 3 | 8 | 8 | 8 | pIC50 | 1 |
Homo sapiens | Glycogen synthase kinase-3 alpha | 8.2 | 8.2 | 8.2 | pKd | 1 |
Homo sapiens | Glycogen synthase kinase-3 beta | 9 | 9 | 9 | pIC50 | 1 |
Homo sapiens | Glycogen synthase kinase-3 beta | 8.2 | 8.2 | 8.2 | pKd | 1 |
Homo sapiens | G protein-coupled receptor kinase 6 | 4.9 | 4.9 | 4.9 | pKd | 1 |
Homo sapiens | Hepatocyte growth factor receptor | 8.2 | 8.2 | 8.2 | pKd | 1 |
Homo sapiens | Inhibitor of nuclear factor kappa B kinase epsilon subunit | 6.7 | 6.7 | 6.7 | pKd | 1 |
Homo sapiens | LIM domain kinase 1 | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | LIM domain kinase 2 | 5.4 | 5.4 | 5.4 | pKd | 1 |
Homo sapiens | MAP kinase-activated protein kinase 5 | 6.2 | 6.2 | 6.2 | pKd | 1 |
Homo sapiens | MAP/microtubule affinity-regulating kinase 2 | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Maternal embryonic leucine zipper kinase | 6.2 | 6.2 | 6.2 | pIC50 | 1 |
Homo sapiens | Maternal embryonic leucine zipper kinase | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase 1 | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase 11 | 7.3 | 7.3 | 7.3 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase 2 | 6.6 | 6.6 | 6.6 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase 3 | 6.5 | 6.5 | 6.5 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase 5 | 4.6 | 4.6 | 4.6 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 1 | 6.7 | 6.7 | 6.7 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 4 | 7 | 7 | 7 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 5 | 5.7 | 5.7 | 5.7 | pKd | 1 |
Homo sapiens | Mitotic checkpoint serine/threonine-protein kinase BUB1 | 7 | 7 | 7 | pKd | 1 |
Homo sapiens | Myosin light chain kinase | 6.9 | 6.9 | 6.9 | pKd | 1 |
Homo sapiens | Platelet-derived growth factor receptor alpha | 8 | 8 | 8 | pIC50 | 1 |
Homo sapiens | Protein kinase C alpha | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Protein kinase C beta | 5.5 | 5.5 | 5.5 | pKd | 1 |
Homo sapiens | Protein kinase C mu | 8 | 8 | 8 | pIC50 | 1 |
Homo sapiens | Protein kinase C nu | 6.3 | 6.3 | 6.3 | pKd | 1 |
Homo sapiens | Protein kinase N1 | 5.5 | 5.5 | 5.5 | pKd | 1 |
Homo sapiens | Protein kinase N2 | 5.6 | 5.6 | 5.6 | pKd | 1 |
Homo sapiens | Proto-oncogene tyrosine-protein kinase MER | 9 | 9 | 9 | pIC50 | 1 |
Homo sapiens | Pyruvate dehydrogenase kinase isoform 1 | 8 | 8 | 8 | pIC50 | 1 |
Homo sapiens | Ribosomal protein S6 kinase 1 | 6.9 | 6.9 | 6.9 | pKd | 1 |
Homo sapiens | Ribosomal protein S6 kinase alpha 1 | 6.3 | 6.3 | 6.3 | pKd | 2 |
Homo sapiens | Ribosomal protein S6 kinase alpha 2 | 9 | 9 | 9 | pIC50 | 2 |
Homo sapiens | Ribosomal protein S6 kinase alpha 3 | 9 | 9 | 9 | pIC50 | 2 |
Homo sapiens | Ribosomal protein S6 kinase alpha 3 | 7 | 7 | 7 | pKd | 2 |
Homo sapiens | Ribosomal protein S6 kinase alpha 4 | 8 | 8 | 8 | pIC50 | 2 |
Homo sapiens | Ribosomal protein S6 kinase alpha 4 | 7.1 | 7.1 | 7.1 | pKd | 2 |
Homo sapiens | Ribosomal protein S6 kinase alpha 5 | 5.9 | 5.9 | 5.9 | pKd | 2 |
Homo sapiens | Ribosomal protein S6 kinase alpha 6 | 7.8 | 7.8 | 7.8 | pKd | 2 |
Homo sapiens | Serine/threonine-protein kinase 10 | 7.1 | 7.1 | 7.1 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase 16 | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase 17A | 8 | 8 | 8 | pIC50 | 1 |
Homo sapiens | Serine/threonine-protein kinase 2 | 6.4 | 6.4 | 6.4 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase Aurora-A | 8.5 | 8.5 | 8.5 | pIC50 | 2 |
Homo sapiens | Serine/threonine-protein kinase Aurora-A | 7.3 | 7.3 | 7.8 | pKd | 2 |
Homo sapiens | Serine/threonine-protein kinase Aurora-B | 7.5 | 7.5 | 8.6 | pIC50 | 4 |
Homo sapiens | Serine/threonine-protein kinase Aurora-B | 7.8 | 7.8 | 7.8 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase Chk1 | 7.1 | 7.1 | 7.1 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase c-TAK1 | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase D2 | 6.6 | 6.6 | 6.6 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase GAK | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase LATS1 | 7.4 | 7.4 | 7.4 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase Nek3 | 5.7 | 5.7 | 5.7 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase NEK9 | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase PAK 4 | 7 | 7 | 7 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase PAK6 | 6.7 | 6.7 | 6.7 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase PCTAIRE-1 | 7.5 | 7.5 | 7.5 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase PCTAIRE-2 | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase PLK4 | 7.7 | 7.7 | 7.7 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase receptor R3 | 7.8 | 7.8 | 7.8 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase SIK2 | 7.5 | 7.5 | 7.5 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase SIK3 | 5.4 | 5.4 | 5.4 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase TAO1 | 5.7 | 5.7 | 5.7 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase TBK1 | 7 | 7 | 7 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase ULK3 | 7.4 | 7.4 | 7.4 | pKd | 1 |
Homo sapiens | TGF-beta receptor type I | 7.1 | 7.1 | 7.1 | pKd | 1 |
Homo sapiens | TGF-beta receptor type II | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | TRAF2- and NCK-interacting kinase | 6.1 | 6.1 | 6.1 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase ABL | 8.4 | 8 | 8.4 | pIC50 | 3 |
Homo sapiens | Tyrosine-protein kinase ABL | 6.5 | 6.5 | 6.5 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase ABL2 | 6 | 6 | 6 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase BRK | 6.7 | 6.7 | 6.7 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase BTK | 6.3 | 6.3 | 6.3 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase CSK | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase FER | 6.5 | 6.5 | 6.5 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase FGR | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase FYN | 6.3 | 6.3 | 6.3 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase HCK | 6.2 | 6.2 | 6.2 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase JAK1 | 6.4 | 6.4 | 6.4 | pKd | 2 |
Homo sapiens | Tyrosine-protein kinase JAK2 | 8.9 | 8.9 | 9 | pIC50 | 4 |
Homo sapiens | Tyrosine-protein kinase JAK2 | 8 | 8 | 8 | pKd | 2 |
Homo sapiens | Tyrosine-protein kinase JAK3 | 9 | 9 | 9 | pIC50 | 4 |
Homo sapiens | Tyrosine-protein kinase LCK | 6.1 | 6.1 | 6.1 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase Lyn | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase receptor FLT3 | 8 | 8 | 8 | pIC50 | 2 |
Homo sapiens | Tyrosine-protein kinase receptor FLT3 | 7.2 | 7.2 | 7.2 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase receptor RET | 9 | 9 | 9 | pIC50 | 1 |
Homo sapiens | Tyrosine-protein kinase receptor RET | 8 | 8 | 8 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase SRC | 8 | 8 | 8 | pIC50 | 1 |
Homo sapiens | Tyrosine-protein kinase SRC | 6.2 | 6.2 | 6.2 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase SYK | 6.9 | 6.9 | 6.9 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase TEC | 6.9 | 6.9 | 6.9 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase TYK2 | 9 | 9 | 9 | pIC50 | 2 |
Homo sapiens | Tyrosine-protein kinase TYK2 | 6.6 | 6.6 | 6.6 | pKd | 2 |
Homo sapiens | Tyrosine-protein kinase YES | 9 | 9 | 9 | pIC50 | 1 |
Homo sapiens | Tyrosine-protein kinase YES | 6.2 | 6.2 | 6.2 | pKd | 1 |
Homo sapiens | Uncharacterized aarF domain-containing protein kinase 1 | 6.3 | 6.3 | 6.3 | pKd | 1 |
Homo sapiens | Vascular endothelial growth factor receptor 1 | 8 | 8 | 8 | pIC50 | 1 |
Homo sapiens | Vascular endothelial growth factor receptor 2 | 8 | 8 | 8 | pIC50 | 1 |
Homo sapiens | Vascular endothelial growth factor receptor 3 | 9 | 9 | 9 | pIC50 | 1 |