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  2IVU - chain A | Ret proto-oncogene
Structure information
PDB:2IVU
PubMed:16928683
Release date:2006-08-10
Resolution:2.5 Å
 
Kinase:RET
Family:Ret
Group:TK
Species:HUMAN
 
Quality Score:8
Missing Residues:0
Missing Atoms:26
DFG conformation:in
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes (2.7Å)
 
 
ASP rotation (xDFG.81) :9°
PHE rotation (xDFG.82) :16°
Activation loop position:-3.2Å
αC-helix position:16.4Å
 
G-rich loop angle:47.8°
G-rich loop distance:14.8Å
G-rich loop rotation:47°
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond ligand
H-bond protein
I5
H-bond protein
I10
H-bond protein
Binding pocket sequence
UniprotKTLGEGEFGKVVKVAVKMLDLLSEFNVLKQVNPHVIKLYGALLIVEYAKYGSLRGFLREYLAEMKLVHRDLAARNILVISDFGLS
Structure:KTLGEGEFGKVVKVAVKMLDLLSEFNVLKQVNPHVIKLYGALLIVEYAKYGSLRGFLREYLAEMKLVHRDLAARNILVISDFGLS


Modified residues
Residue 905 (not in pocket)
Phosphorylated tyrosine
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: ZD6
Ligand Name: 4-BROMO-2-FLUORO-N-[(4E)-6-METHOXY-7-[(1-METHYLPIPERIDIN-4-YL)METHOXY]QUINAZOLIN-4(1H)-YLIDENE]ANILINE

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  • LABELS
  • KLIFS residue #
  • Amino Acid
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  • COLORS
  • Interaction types
  • KLIFS (all res.)
  • KLIFS (interacting res.)
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  • 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 K
728		2 T
729		3 L
730		4 G
731		5 E
732		6 G
733		7 E
734		8 F
735		9 G
736		10 K
737		11 V
738		12 V
739		13 K
740		14 V
755		15 A
756		16 V
757		17 K
758		18 M
759		19 L
760		20 D
771
■■■■■■
αC b.l IV
21 L
772		22 L
773		23 S
774		24 E
775		25 F
776		26 N
777		27 V
778		28 L
779		29 K
780		30 Q
781		31 V
782		32 N
783		33 P
785		34 H
786		35 V
787		36 I
788		37 K
789		38 L
790		39 Y
791		40 G
792
■■■
IV V GK hinge linker αD αE
41 A
793		42 L
801		43 L
802		44 I
803		45 V
804		46 E
805		47 Y
806		48 A
807		49 K
808		50 Y
809		51 G
810		52 S
811		53 L
812		54 R
813		55 G
814		56 F
815		57 L
816		58 R
817		59 E
818		60 Y
864
■■■■♦■▲■■■
αE VI c.l VII VIII x
61 L
865		62 A
866		63 E
867		64 M
868		65 K
869		66 L
870		67 V
871		68 H
872		69 R
873		70 D
874		71 L
875		72 A
876		73 A
877		74 R
878		75 N
879		76 I
880		77 L
881		78 V
882		79 I
890		80 S
891
■
DFG a.l
81 D
892		82 F
893		83 G
894		84 L
895		85 S
896

Interaction pattern search
Search KLIFS for kinase-ligand complexes with similar interaction patterns:
Specify the minimum similarity (0.00 no similarity, 1.00 identical)
Binding affinities
ChEMBL ID:CHEMBL24828
Bioaffinities: 440 records for 113 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensActivin receptor type-16.86.86.8pKd2
Homo sapiensActivin receptor type-16.76.76.7pKi1
Homo sapiensALK tyrosine kinase receptor5.75.75.7pKd2
Homo sapiensALK tyrosine kinase receptor5.85.85.8pKi1
Homo sapiensAMP-activated protein kinase, alpha-1 subunit555.5pKd2
Homo sapiensBone morphogenetic protein receptor type-1B6.66.66.6pKd1
Homo sapiensBreakpoint cluster region protein6.16.16.1pKd2
Homo sapiensCasein kinase I epsilon5.55.55.8pKd3
Homo sapiensChaperone activity of bc1 complex-like, mitochondrial5.45.45.4pKd2
Homo sapiensCitron Rho-interacting kinase5.85.85.8pKd2
Homo sapiensCyclin-dependent kinase 75.45.45.4pKd1
Homo sapiensDiscoidin domain-containing receptor 26.56.56.5pKd2
Homo sapiensDual specificity mitogen-activated protein kinase kinase 15.85.85.8pKd2
Homo sapiensDual specificity mitogen-activated protein kinase kinase 1666pKi1
Homo sapiensDual specificity mitogen-activated protein kinase kinase 2666pKd2
Homo sapiensDual specificity mitogen-activated protein kinase kinase 25.85.85.8pKi1
Homo sapiensDual specificity mitogen-activated protein kinase kinase 57.37.37.3pKd1
Homo sapiensDual specificity testis-specific protein kinase 15.45.45.4pKd2
Homo sapiensEphrin type-A receptor 16.66.66.6pKd2
Homo sapiensEphrin type-A receptor 265.76pKd3
Homo sapiensEphrin type-A receptor 35.75.75.8pKd3
Homo sapiensEphrin type-A receptor 45.85.45.8pKd3
Homo sapiensEphrin type-A receptor 56.66.56.6pKd3
Homo sapiensEphrin type-A receptor 67.37.27.3pKd3
Homo sapiensEphrin type-A receptor 75.65.55.6pKd3
Homo sapiensEphrin type-A receptor 876.87pKd3
Homo sapiensEphrin type-B receptor 16.56.36.5pKd3
Homo sapiensEphrin type-B receptor 26.46.46.4pKd2
Homo sapiensEphrin type-B receptor 46.35.66.3pKd3
Homo sapiensEphrin type-B receptor 67.17.17.1pKd1
Homo sapiensEpidermal growth factor receptor erbB16.36.18pIC5016
Homo sapiensEpidermal growth factor receptor erbB185.48.3pKd25
Homo sapiensEpithelial discoidin domain-containing receptor 185.98pKd3
Homo sapiensFibroblast growth factor receptor 15.35.25.6pIC504
Homo sapiensFibroblast growth factor receptor 16.35.36.3pKd3
Homo sapiensFibroblast growth factor receptor 15.75.75.7pKi1
Homo sapiensFibroblast growth factor receptor 265.36pKd3
Homo sapiensFibroblast growth factor receptor 35.85.26.6pKd5
Homo sapiensFibroblast growth factor receptor 45.65.65.6pKd1
Homo sapiensHepatocyte growth factor receptor5.25.25.4pKd3
Homo sapiensHormonally up-regulated neu tumor-associated kinase5.45.45.4pKd1
Homo sapiensInterleukin-1 receptor-associated kinase 15.95.95.9pKd1
Homo sapiensInterleukin-1 receptor-associated kinase 47.17.17.1pKd1
Homo sapiensLeucine-rich repeat serine/threonine-protein kinase 25.75.75.7pKi1
Homo sapiensLeukocyte tyrosine kinase receptor6.36.36.3pKd2
Homo sapiensLeukocyte tyrosine kinase receptor6.46.46.4pKi1
Homo sapiensMacrophage colony stimulating factor receptor5.85.85.8pIC501
Homo sapiensMacrophage colony stimulating factor receptor5.95.95.9pKd2
Homo sapiensMacrophage-stimulating protein receptor5.55.55.5pIC501
Homo sapiensMAP kinase-interacting serine/threonine-protein kinase MNK16.46.46.4pKd2
Homo sapiensMAP kinase p38 alpha5.65.65.6pKi1
Homo sapiensMAP kinase signal-integrating kinase 25.85.55.8pKd3
Homo sapiensMisshapen-like kinase 15.55.55.5pKd1
Homo sapiensMitogen-activated protein kinase 65.85.85.8pKd2
Homo sapiensMitogen-activated protein kinase kinase kinase 45.35.35.5pKd2
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 15.35.35.3pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 25.85.85.8pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 35.85.85.8pKd2
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 45.95.95.9pKd2
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 46.86.86.8pKi1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 56.46.36.4pKd3
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 56.56.56.5pKi1
Homo sapiensMixed lineage kinase 75.35.35.3pKd2
Homo sapiensPhosphorylase kinase gamma subunit 165.26pKd3
Homo sapiensPhosphorylase kinase gamma subunit 2555.1pKd2
Homo sapiensPlatelet-derived growth factor receptor alpha6.66.66.6pKd2
Homo sapiensPlatelet-derived growth factor receptor alpha6.86.86.8pKi1
Homo sapiensPlatelet-derived growth factor receptor beta666.3pIC502
Homo sapiensPlatelet-derived growth factor receptor beta7.16.67.1pKd3
Homo sapiensPlatelet-derived growth factor receptor beta666pKi1
Homo sapiensProto-oncogene tyrosine-protein kinase MER5.95.95.9pKd3
Homo sapiensReceptor-interacting serine/threonine-protein kinase 46.26.26.2pKd1
Homo sapiensReceptor protein-tyrosine kinase erbB-25.65.65.6pKd2
Homo sapiensReceptor protein-tyrosine kinase erbB-46.36.36.3pKd1
Homo sapiensReceptor tyrosine-protein kinase erbB-36.86.86.8pKd1
Homo sapiensRho-associated protein kinase 25.45.45.4pKd1
Homo sapiensRho-associated protein kinase 2777pKi1
Homo sapiensRibosomal protein S6 kinase 15.85.85.8pKd1
Homo sapiensRibosomal protein S6 kinase alpha 16.46.46.4pKd4
Homo sapiensRibosomal protein S6 kinase alpha 66.66.66.6pKd4
Homo sapiensSerine/threonine-protein kinase 107.15.57.1pKd5
Homo sapiensSerine/threonine-protein kinase 2777pKd3
Homo sapiensSerine/threonine-protein kinase 32A5.35.35.3pKd1
Homo sapiensSerine/threonine-protein kinase 335.95.95.9pKd2
Homo sapiensSerine/threonine-protein kinase 357.37.37.3pKd1
Homo sapiensSerine/threonine-protein kinase Aurora-B5.65.65.6pKi1
Homo sapiensSerine/threonine-protein kinase Aurora-C5.85.85.8pKd2
Homo sapiensSerine/threonine-protein kinase GAK7.16.57.1pKd4
Homo sapiensSerine/threonine-protein kinase MRCK-A5.65.65.6pKd2
Homo sapiensSerine/threonine-protein kinase MRCK beta5.65.65.6pKd2
Homo sapiensSerine/threonine-protein kinase MRCK gamma5.75.75.7pKd2
Homo sapiensSerine/threonine-protein kinase PLK46.25.86.2pKd3
Homo sapiensSerine/threonine-protein kinase receptor R36.36.36.3pKd2
Homo sapiensSerine/threonine-protein kinase RIPK27.57.18.3pKd4
Homo sapiensSerine/threonine-protein kinase SIK15.75.75.7pKd2
Homo sapiensSerine/threonine-protein kinase SIK26.46.46.4pKd2
Homo sapiensSerine/threonine-protein kinase SIK35.45.45.4pKd1
Homo sapiensSerine/threonine-protein kinase TNNI3K5.65.65.6pKd2
Homo sapiensSerine/threonine-protein kinase ULK35.25.25.2pKd1
Homo sapiensSPS1/STE20-related protein kinase YSK4666pKd1
Homo sapiensStem cell growth factor receptor6.56.56.5pIC501
Homo sapiensStem cell growth factor receptor6.55.77.5pKd16
Homo sapiensTRAF2- and NCK-interacting kinase5.65.45.6pKd3
Homo sapiensTyrosine-protein kinase ABL6.86.87.1pIC502
Homo sapiensTyrosine-protein kinase ABL75.98.1pKd30
Homo sapiensTyrosine-protein kinase ABL7.57.57.5pKi1
Homo sapiensTyrosine-protein kinase ABL27.26.97.2pKd3
Homo sapiensTyrosine-protein kinase BLK7.27.27.2pKd2
Homo sapiensTyrosine-protein kinase BRK6.85.97.5pKd4
Homo sapiensTyrosine-protein kinase BTK5.85.85.8pKd1
Homo sapiensTyrosine-protein kinase BTK5.95.95.9pKi1
Homo sapiensTyrosine-protein kinase CSK5.65.45.6pKd3
Homo sapiensTyrosine-protein kinase FGR6.65.76.6pKd3
Homo sapiensTyrosine-protein kinase FRK6.36.36.8pKd4
Homo sapiensTyrosine-protein kinase FYN6.45.26.4pKd3
Homo sapiensTyrosine-protein kinase FYN6.26.26.2pKi1
Homo sapiensTyrosine-protein kinase HCK6.45.46.4pKd3
Homo sapiensTyrosine-protein kinase LCK7.25.57.8pKd4
Homo sapiensTyrosine-protein kinase LCK7.47.47.4pKi1
Homo sapiensTyrosine-protein kinase Lyn76.27pKd3
Homo sapiensTyrosine-protein kinase receptor FLT36.15.86.7pKd13
Homo sapiensTyrosine-protein kinase receptor RET75.87.3pIC506
Homo sapiensTyrosine-protein kinase receptor RET7.56.37.9pKd5
Homo sapiensTyrosine-protein kinase receptor RET7.77.77.7pKi1
Homo sapiensTyrosine-protein kinase receptor Tie-15.85.85.8pKd2
Homo sapiensTyrosine-protein kinase receptor TYRO3777pKd3
Homo sapiensTyrosine-protein kinase receptor TYRO37.27.27.2pKi1
Homo sapiensTyrosine-protein kinase receptor UFO6.66.66.6pKd3
Homo sapiensTyrosine-protein kinase receptor UFO6.66.66.6pKi1
Homo sapiensTyrosine-protein kinase SRC6.76.77.4pIC502
Homo sapiensTyrosine-protein kinase SRC7.26.87.2pKd3
Homo sapiensTyrosine-protein kinase Srms5.75.75.7pKd2
Homo sapiensTyrosine-protein kinase TIE-25.65.66.3pIC502
Homo sapiensTyrosine-protein kinase TIE-265.46pKd3
Homo sapiensTyrosine-protein kinase TXK5.45.45.4pKd2
Homo sapiensTyrosine-protein kinase YES6.96.66.9pKd3
Homo sapiensUncharacterized aarF domain-containing protein kinase 45.85.85.8pKd2
Homo sapiensVascular endothelial growth factor receptor 175.87.7pIC508
Homo sapiensVascular endothelial growth factor receptor 16.66.66.6pKd2
Homo sapiensVascular endothelial growth factor receptor 17.27.27.2pKi1
Homo sapiensVascular endothelial growth factor receptor 27.45.28.1pIC5041
Homo sapiensVascular endothelial growth factor receptor 26.16.16.3pKd3
Homo sapiensVascular endothelial growth factor receptor 28.28.28.2pKi1
Homo sapiensVascular endothelial growth factor receptor 36.66.66.6pIC501
Homo sapiensVascular endothelial growth factor receptor 3666.5pKd3
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