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

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
O1
H-bond protein
Binding pocket sequence
UniprotGYTGQGVFSNVVRVAVKIITGLKELEFLKKLNFHCLRLFRHCLVFEPLS-MNLREVLKKLLKRCNILHADIKPDNILVLCDFGSA
Structure:GYTGQGVFSNVVRVAVKIITGLKELEFLKKLNFHCLRLLRHCLVFEPLS_MNLREVLKKLLKRCNILHADIKPDNILVLCDF___


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the 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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  • KLIFS residue #
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  • COLORS
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  • KLIFS (all res.)
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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 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 _
_

Interaction pattern search
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Binding affinities
ChEMBL ID:CHEMBL1738757
Bioaffinities: 68 records for 63 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensBreakpoint cluster region protein6.46.46.4pKd2
Homo sapiensc-Jun N-terminal kinase 14.64.64.6pKd1
Homo sapiensc-Jun N-terminal kinase 2666pKd1
Homo sapiensc-Jun N-terminal kinase 37.17.17.1pKd1
Homo sapiensCyclin-dependent kinase 1666pKd1
Homo sapiensCyclin-dependent kinase 26.76.76.7pKd1
Homo sapiensCyclin-dependent kinase 35.65.65.6pKd1
Homo sapiensCyclin-dependent kinase 45.85.85.8pKd1
Homo sapiensCyclin-dependent kinase 55.85.85.8pKd1
Homo sapiensDiscoidin domain-containing receptor 26.16.16.1pKd1
Homo sapiensDual specificity protein kinase CLK45.65.65.6pKd1
Homo sapiensDual specificity testis-specific protein kinase 28.78.78.7pKd1
Homo sapiensDual specificty protein kinase CLK15.75.75.7pKd1
Homo sapiensEpithelial discoidin domain-containing receptor 16.66.66.6pKd1
Homo sapiensEukaryotic translation initiation factor 2-alpha kinase 16.26.26.2pKd1
Homo sapiensHepatocyte growth factor receptor6.96.96.9pKd1
Homo sapiensInterleukin-1 receptor-associated kinase 15.65.65.6pKd1
Homo sapiensInterleukin-1 receptor-associated kinase 44.64.64.6pKd1
Homo sapiensLIM domain kinase 16.36.36.3pKd1
Homo sapiensLIM domain kinase 25.55.55.5pKd1
Homo sapiensMacrophage-stimulating protein receptor6.16.16.1pKd1
Homo sapiensMAP kinase-activated protein kinase 25.35.35.3pKd1
Homo sapiensMAP kinase p38 alpha5.65.65.6pKd1
Homo sapiensMitogen-activated protein kinase 156.66.66.6pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase 115.55.55.5pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 16.36.36.3pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 2666pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 45.65.65.6pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 55.45.45.4pKd1
Homo sapiensMixed lineage kinase 76.46.46.4pKd1
Homo sapiensMyosin light chain kinase, smooth muscle5.75.75.7pKd1
Homo sapiensNerve growth factor receptor Trk-A6.66.66.6pKd1
Homo sapiensNon-receptor tyrosine-protein kinase TNK17.37.37.3pKd1
Homo sapiensProtein tyrosine kinase 2 beta555pKd1
Homo sapiensReceptor-interacting serine/threonine-protein kinase 35.95.95.9pKd1
Homo sapiensRibosomal protein S6 kinase alpha 44.94.94.9pKd2
Homo sapiensSerine/threonine-protein kinase A-Raf4.54.54.5pKd1
Homo sapiensSerine/threonine-protein kinase B-raf4.64.64.6pKd1
Homo sapiensSerine/threonine-protein kinase/endoribonuclease IRE15.55.55.5pKd1
Homo sapiensSerine/threonine-protein kinase MST14.64.64.6pKd1
Homo sapiensSerine/threonine-protein kinase MST24.94.94.9pKd1
Homo sapiensSerine/threonine-protein kinase PCTAIRE-16.56.56.5pKd1
Homo sapiensSerine/threonine-protein kinase PCTAIRE-28.28.28.2pKd1
Homo sapiensSerine/threonine-protein kinase PLK45.45.45.4pKd1
Homo sapiensSerine/threonine-protein kinase TAO34.94.94.9pKd1
Homo sapiensTRAF2- and NCK-interacting kinase5.75.75.7pKd1
Homo sapiensTyrosine-protein kinase ABL6.56.56.5pKd1
Homo sapiensTyrosine-protein kinase ABL26.96.96.9pKd1
Homo sapiensTyrosine-protein kinase BTK5.95.95.9pKd1
Homo sapiensTyrosine-protein kinase CSK6.46.46.4pKd1
Homo sapiensTyrosine-protein kinase FER5.95.95.9pKd1
Homo sapiensTyrosine-protein kinase FES6.26.26.2pKd1
Homo sapiensTyrosine-protein kinase FRK5.85.85.8pKd1
Homo sapiensTyrosine-protein kinase FYN5.95.95.9pKd1
Homo sapiensTyrosine-protein kinase HCK6.86.86.8pKd1
Homo sapiensTyrosine-protein kinase JAK25.45.45.4pKd2
Homo sapiensTyrosine-protein kinase LCK6.86.86.8pKd1
Homo sapiensTyrosine-protein kinase Lyn6.36.36.3pKd1
Homo sapiensTyrosine-protein kinase receptor FLT36.16.16.1pKd1
Homo sapiensTyrosine-protein kinase receptor RET5.95.95.9pKd1
Homo sapiensTyrosine-protein kinase SRC5.25.25.2pKd1
Homo sapiensTyrosine-protein kinase SYK5.75.75.7pKd1
Homo sapiensTyrosine-protein kinase YES8.68.68.8pIC502
Homo sapiensTyrosine-protein kinase YES5.85.85.8pKd1