6CNH - chain A (model B) | Pre-mRNA processing factor 4B
Structure information
PDB: | 6CNH |
PubMed: | - |
Release date: | 2018-03-28 |
Resolution: | 2 Å |
Kinase: | PRPF4B (PRP4) |
Family: | DYRK |
Group: | CMGC |
Species: | HUMAN |
Quality Score: | 8 |
Missing Residues: | 3 |
Missing Atoms: | 8 |
DFG conformation: | out |
αC-helix conformation: | in |
Salt bridge KIII.17 and EαC.24: | Yes (2.7Å) |
ASP rotation (xDFG.81) : | 211° |
PHE rotation (xDFG.82) : | 203° |
Activation loop position: | 2Å |
αC-helix position: | 18.1Å |
G-rich loop angle: | 57.3° |
G-rich loop distance: | 17.2Å |
G-rich loop rotation: | 64.2° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
O1
H-bond protein
Binding pocket sequence
Uniprot | GYTGQGVFSNVVRVAVKIITGLKELEFLKKLNFHCLRLFRHCLVFEPLS-MNLREVLKKLLKRCNILHADIKPDNILVLCDFGSA |
Structure: | GYTGQGVFSNVVRVAVKIITGLKELEFLKKLNFHCLRLLRHCLVFEPLS_MNLREVLKKLLKRCNILHADIKPDNILVLCDF___ |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: 919
Ligand Name: 4-[4-({[3-tert-butyl-1-(quinolin-6-yl)-1H-pyrazol-5-yl]carbamoyl}amino)-3-fluorophenoxy]-N-methylpyridine-2-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 G 691 | 2 Y 692 | 3 T 693 | 4 G 694 | 5 Q 695 | 6 G 696 | 7 V 697 | 8 F 698 | 9 S 699 | 10 N 700 | 11 V 701 | 12 V 702 | 13 R 703 | 14 V 714 | 15 A 715 | 16 V 716 | 17 K 717 | 18 I 718 | 19 I 719 | 20 T 728 |
■ | ■▲ | ■ | ■ | ■ | ■ | ■ | |||||||||||||
αC | b.l | IV | |||||||||||||||||
21 G 729 | 22 L 730 | 23 K 731 | 24 E 732 | 25 L 733 | 26 E 734 | 27 F 735 | 28 L 736 | 29 K 737 | 30 K 738 | 31 L 739 | 32 N 740 | 33 F 748 | 34 H 749 | 35 C 750 | 36 L 751 | 37 R 752 | 38 L 753 | 39 L 754 | 40 R 755 |
■ | ■▲ | ■ | ■ | ■ | ■ | ■ | |||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 H 756 | 42 C 764 | 43 L 765 | 44 V 766 | 45 F 767 | 46 E 768 | 47 P 769 | 48 L 770 | 49 S 771 | 50 _ _ | 51 M 772 | 52 N 773 | 53 L 774 | 54 R 775 | 55 E 776 | 56 V 777 | 57 L 778 | 58 K 779 | 59 K 780 | 60 L 805 |
■♦ | ■ | ■ | ■▲ | ||||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 L 806 | 62 K 807 | 63 R 808 | 64 C 809 | 65 N 810 | 66 I 811 | 67 L 812 | 68 H 813 | 69 A 814 | 70 D 815 | 71 I 816 | 72 K 817 | 73 P 818 | 74 D 819 | 75 N 820 | 76 I 821 | 77 L 822 | 78 V 823 | 79 L 832 | 80 C 833 |
■ | ■ | ■ | ■ | ■ | ■ | ||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 834 | 82 F 835 | 83 _ _ | 84 _ _ | 85 _ _ | |||||||||||||||
■▲ | ■♦ |
Binding affinities
ChEMBL ID:CHEMBL1738757Bioaffinities: 68 records for 63 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Breakpoint cluster region protein | 6.4 | 6.4 | 6.4 | pKd | 2 |
Homo sapiens | c-Jun N-terminal kinase 1 | 4.6 | 4.6 | 4.6 | pKd | 1 |
Homo sapiens | c-Jun N-terminal kinase 2 | 6 | 6 | 6 | pKd | 1 |
Homo sapiens | c-Jun N-terminal kinase 3 | 7.1 | 7.1 | 7.1 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 1 | 6 | 6 | 6 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 2 | 6.7 | 6.7 | 6.7 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 3 | 5.6 | 5.6 | 5.6 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 4 | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 5 | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Discoidin domain-containing receptor 2 | 6.1 | 6.1 | 6.1 | pKd | 1 |
Homo sapiens | Dual specificity protein kinase CLK4 | 5.6 | 5.6 | 5.6 | pKd | 1 |
Homo sapiens | Dual specificity testis-specific protein kinase 2 | 8.7 | 8.7 | 8.7 | pKd | 1 |
Homo sapiens | Dual specificty protein kinase CLK1 | 5.7 | 5.7 | 5.7 | pKd | 1 |
Homo sapiens | Epithelial discoidin domain-containing receptor 1 | 6.6 | 6.6 | 6.6 | pKd | 1 |
Homo sapiens | Eukaryotic translation initiation factor 2-alpha kinase 1 | 6.2 | 6.2 | 6.2 | pKd | 1 |
Homo sapiens | Hepatocyte growth factor receptor | 6.9 | 6.9 | 6.9 | pKd | 1 |
Homo sapiens | Interleukin-1 receptor-associated kinase 1 | 5.6 | 5.6 | 5.6 | pKd | 1 |
Homo sapiens | Interleukin-1 receptor-associated kinase 4 | 4.6 | 4.6 | 4.6 | pKd | 1 |
Homo sapiens | LIM domain kinase 1 | 6.3 | 6.3 | 6.3 | pKd | 1 |
Homo sapiens | LIM domain kinase 2 | 5.5 | 5.5 | 5.5 | pKd | 1 |
Homo sapiens | Macrophage-stimulating protein receptor | 6.1 | 6.1 | 6.1 | pKd | 1 |
Homo sapiens | MAP kinase-activated protein kinase 2 | 5.3 | 5.3 | 5.3 | pKd | 1 |
Homo sapiens | MAP kinase p38 alpha | 5.6 | 5.6 | 5.6 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase 15 | 6.6 | 6.6 | 6.6 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase 11 | 5.5 | 5.5 | 5.5 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 1 | 6.3 | 6.3 | 6.3 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 2 | 6 | 6 | 6 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 4 | 5.6 | 5.6 | 5.6 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 5 | 5.4 | 5.4 | 5.4 | pKd | 1 |
Homo sapiens | Mixed lineage kinase 7 | 6.4 | 6.4 | 6.4 | pKd | 1 |
Homo sapiens | Myosin light chain kinase, smooth muscle | 5.7 | 5.7 | 5.7 | pKd | 1 |
Homo sapiens | Nerve growth factor receptor Trk-A | 6.6 | 6.6 | 6.6 | pKd | 1 |
Homo sapiens | Non-receptor tyrosine-protein kinase TNK1 | 7.3 | 7.3 | 7.3 | pKd | 1 |
Homo sapiens | Protein tyrosine kinase 2 beta | 5 | 5 | 5 | pKd | 1 |
Homo sapiens | Receptor-interacting serine/threonine-protein kinase 3 | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Ribosomal protein S6 kinase alpha 4 | 4.9 | 4.9 | 4.9 | pKd | 2 |
Homo sapiens | Serine/threonine-protein kinase A-Raf | 4.5 | 4.5 | 4.5 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase B-raf | 4.6 | 4.6 | 4.6 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase/endoribonuclease IRE1 | 5.5 | 5.5 | 5.5 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase MST1 | 4.6 | 4.6 | 4.6 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase MST2 | 4.9 | 4.9 | 4.9 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase PCTAIRE-1 | 6.5 | 6.5 | 6.5 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase PCTAIRE-2 | 8.2 | 8.2 | 8.2 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase PLK4 | 5.4 | 5.4 | 5.4 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase TAO3 | 4.9 | 4.9 | 4.9 | pKd | 1 |
Homo sapiens | TRAF2- and NCK-interacting kinase | 5.7 | 5.7 | 5.7 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase ABL | 6.5 | 6.5 | 6.5 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase ABL2 | 6.9 | 6.9 | 6.9 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase BTK | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase CSK | 6.4 | 6.4 | 6.4 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase FER | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase FES | 6.2 | 6.2 | 6.2 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase FRK | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase FYN | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase HCK | 6.8 | 6.8 | 6.8 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase JAK2 | 5.4 | 5.4 | 5.4 | pKd | 2 |
Homo sapiens | Tyrosine-protein kinase LCK | 6.8 | 6.8 | 6.8 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase Lyn | 6.3 | 6.3 | 6.3 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase receptor FLT3 | 6.1 | 6.1 | 6.1 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase receptor RET | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase SRC | 5.2 | 5.2 | 5.2 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase SYK | 5.7 | 5.7 | 5.7 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase YES | 8.6 | 8.6 | 8.8 | pIC50 | 2 |
Homo sapiens | Tyrosine-protein kinase YES | 5.8 | 5.8 | 5.8 | pKd | 1 |