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  5VC5 - chain A (model A) | WEE1 G2 checkpoint kinase
Structure information
PDB:5VC5
PubMed:28792760
Release date:2017-08-23
Resolution:1.93 Å
 
Kinase:WEE1 (Wee1)
Family:WEE
Group:Other
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:No (5.1Å)
 
 
ASP rotation (xDFG.81) :343°
PHE rotation (xDFG.82) :338°
Activation loop position:-3.4Å
αC-helix position:17.2Å
 
G-rich loop angle:62.5°
G-rich loop distance:18.7Å
G-rich loop rotation:49.3°
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I2
H-bond protein
I5
H-bond protein
I9
H-bond protein
Binding pocket sequence
UniprotEKIGSGEFGSVFKYAIKRSNALREVYAHAVLGSHVVRYFSALIQNEYCNGGSLADAISEYIHSMSLVHMDIKPSNIFIIGDLGHV
Structure:EKIGSGEFGSVFKYAIKRSNALREVYAHAVLGSHVVRYFSALIQNEYCNGGSLADAISEYIHSMSLVHMDIKPSNIFIIGDLGHV


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: 96M
Ligand Name: 6-(2,6-dichlorophenyl)-2-({4-[2-(diethylamino)ethoxy]phenyl}amino)-8-methylpyrido[2,3-d]pyrimidin-7(8H)-one

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  • KLIFS residue #
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  • COLORS
  • Interaction types
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  • KLIFS (interacting 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 E
303		2 K
304		3 I
305		4 G
306		5 S
307		6 G
308		7 E
309		8 F
310		9 G
311		10 S
312		11 V
313		12 F
314		13 K
315		14 Y
325		15 A
326		16 I
327		17 K
328		18 R
329		19 S
330		20 N
342
■■■■■
αC b.l IV
21 A
343		22 L
344		23 R
345		24 E
346		25 V
347		26 Y
348		27 A
349		28 H
350		29 A
351		30 V
352		31 L
353		32 G
354		33 S
357		34 H
358		35 V
359		36 V
360		37 R
361		38 Y
362		39 F
363		40 S
364
■■■
IV V GK hinge linker αD αE
41 A
365		42 L
373		43 I
374		44 Q
375		45 N
376		46 E
377		47 Y
378		48 C
379		49 N
380		50 G
381		51 G
382		52 S
383		53 L
384		54 A
385		55 D
386		56 A
387		57 I
388		58 S
389		59 E
390		60 Y
416
■■■■♦■▲▲■■
αE VI c.l VII VIII x
61 I
417		62 H
418		63 S
419		64 M
420		65 S
421		66 L
422		67 V
423		68 H
424		69 M
425		70 D
426		71 I
427		72 K
428		73 P
429		74 S
430		75 N
431		76 I
432		77 F
433		78 I
434		79 I
461		80 G
462
■♦■
DFG a.l
81 D
463		82 L
464		83 G
465		84 H
466		85 V
467
■

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:CHEMBL49120
Bioaffinities: 76 records for 56 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensActivin receptor type-18.88.88.8pKi1
Homo sapiensALK tyrosine kinase receptor5.45.45.4pKi1
Homo sapiensAMP-activated protein kinase, alpha-1 subunit6.56.56.5pKi1
Homo sapienscAMP-dependent protein kinase alpha-catalytic subunit666pKi1
Homo sapiensc-Jun N-terminal kinase 16.86.86.8pKi1
Homo sapiensc-Jun N-terminal kinase 26.46.46.4pKi1
Homo sapiensDual specificity mitogen-activated protein kinase kinase 17.37.37.3pKi1
Homo sapiensDual specificity mitogen-activated protein kinase kinase 26.86.86.8pKi1
Homo sapiensEpidermal growth factor receptor erbB14.44.46.5pIC502
Homo sapiensFibroblast growth factor receptor 17.47.47.4pIC502
Homo sapiensFibroblast growth factor receptor 18.38.38.3pKi1
Homo sapiensFocal adhesion kinase 16.36.36.3pKi1
Homo sapiensHepatocyte growth factor receptor6.86.86.8pKi1
Homo sapiensInhibitor of nuclear factor kappa B kinase epsilon subunit5.65.65.6pKi1
Homo sapiensInsulin-like growth factor I receptor5.75.75.7pKi1
Homo sapiensLeucine-rich repeat serine/threonine-protein kinase 26.66.66.6pKi1
Homo sapiensLeukocyte tyrosine kinase receptor6.46.46.4pKi1
Homo sapiensMacrophage colony stimulating factor receptor9.29.29.2pKi1
Homo sapiensMacrophage-stimulating protein receptor6.46.46.4pKi1
Homo sapiensMAP kinase p38 alpha8.58.58.5pKi1
Homo sapiensMisshapen-like kinase 17.57.57.5pKi1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 26.46.46.4pKi1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 47.17.17.1pKi1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 58.18.18.1pKi1
Homo sapiensNerve growth factor receptor Trk-A5.65.65.6pKi1
Homo sapiensNeurotrophic tyrosine kinase receptor type 25.85.85.8pKi1
Homo sapiensNT-3 growth factor receptor5.65.65.6pKi1
Homo sapiensPlatelet-derived growth factor receptor alpha8.78.78.7pKi1
Homo sapiensPlatelet-derived growth factor receptor beta9.19.19.1pKi1
Mus musculusPlatelet-derived growth factor receptor beta7.17.17.1pIC502
Homo sapiensProtein kinase C nu7.27.27.2pKi1
Homo sapiensRibosomal protein S6 kinase alpha 36.36.36.3pKi2
Homo sapiensSerine/threonine-protein kinase 17A666pKi1
Homo sapiensSerine/threonine-protein kinase Aurora-B5.65.65.6pKi1
Homo sapiensSerine/threonine-protein kinase MST26.16.16.1pKi1
Homo sapiensSerine/threonine-protein kinase PAK 46.26.26.2pKi1
Homo sapiensSerine/threonine-protein kinase PRKX5.65.65.6pKi1
Homo sapiensSerine/threonine-protein kinase TAO18.28.28.2pKi1
Homo sapiensSerine/threonine-protein kinase WEE16.86.86.8pIC501
Homo sapiensSerine/threonine-protein kinase WEE1888pKd1
Homo sapiensSerine/threonine-protein kinase WEE19.39.39.3pKi1
Homo sapiensTyrosine- and threonine-specific cdc2-inhibitory kinase8.17.58.2pIC505
Homo sapiensTyrosine- and threonine-specific cdc2-inhibitory kinase6.66.66.6pKd1
Homo sapiensTyrosine- and threonine-specific cdc2-inhibitory kinase8.78.79.1pKi5
Homo sapiensTyrosine kinase non-receptor protein 28.98.98.9pKi1
Homo sapiensTyrosine-protein kinase ABL9.39.39.3pKi1
Homo sapiensTyrosine-protein kinase BTK888pKi1
Homo sapiensTyrosine-protein kinase FYN8.88.88.8pKi1
Homo sapiensTyrosine-protein kinase JAK27.47.47.4pKi2
Homo sapiensTyrosine-protein kinase JAK36.46.46.4pKi2
Homo sapiensTyrosine-protein kinase LCK8.98.98.9pKi1
Homo sapiensTyrosine-protein kinase receptor FLT36.16.16.1pKi1
Homo sapiensTyrosine-protein kinase receptor RET8.18.18.1pKi1
Homo sapiensTyrosine-protein kinase receptor TYRO38.48.48.4pKi1
Gallus gallusTyrosine-protein kinase SRC8.18.18.1pIC502
Homo sapiensTyrosine-protein kinase SRC8.18.18.1pIC501
Mus musculusTyrosine-protein kinase SRC8.18.18.1pIC501
Homo sapiensTyrosine-protein kinase SYK7.17.17.1pKi1
Homo sapiensVascular endothelial growth factor receptor 17.47.47.4pKi1
Homo sapiensVascular endothelial growth factor receptor 28.18.18.1pKi1
Homo sapiensWee1-like protein kinase 28.38.38.3pKd1
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