4IJP - chain A (model B) | Pre-mRNA processing factor 4B
Structure information
PDB:4IJP
PubMed:24003220
Release date:2013-08-28
Resolution:2.25 Å
 
Kinase:PRPF4B (PRP4)
Family:DYRK
Group:CMGC
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 (2.8Å)
 
 
ASP rotation (xDFG.81) :351°
PHE rotation (xDFG.82) :
Activation loop position:-3.6Å
αC-helix position:17.3Å
 
G-rich loop angle:52.8°
G-rich loop distance:16.4Å
G-rich loop rotation:15.6°
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I3
No H-bonds
I5
H-bond protein
Binding pocket sequence
UniprotGYTGQGVFSNVVRVAVKIITGLKELEFLKKLNFHCLRLFRHCLVFEPLS-MNLREVLKKLLKRCNILHADIKPDNILVLCDFGSA
Structure:GYTGQGVFSNVVRVAVKIITGLKELEFLKKLNFHCLRLFRHCLVFEPLS_MNLREVLKKLLKRCNILHADIKPDNILVLCDFGSA


Modified residues
Residue 849 (not in pocket)
Phosphorylated tyrosine
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: 1EH
Ligand Name: 4-(5-{[(2-chloropyridin-4-yl)methyl]carbamoyl}thiophen-2-yl)-1-benzothiophene-2-carboxamide

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  • LABELS
  • KLIFS residue #
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  • None
  • COLORS
  • Interaction types
  • KLIFS (all res.)
  • KLIFS (interacting res.)
  • None
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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 F
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 G
836
84 S
837
85 A
838

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Binding affinities
Ligand not found in ChEMBL.