Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T49507 Target Info
Target Name Ephrin type-B receptor 4 (EPHB4)
Synonyms Tyrosine-protein kinase TYRO11; TYRO11; MYK1; Hepatoma transmembrane kinase; HTK
Target Type Clinical trial Target
Gene Name EPHB4
Biochemical Class Kinase
UniProt ID
EPHB4_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: Dasatinib Ligand Info
Structure Description Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with Dasatinib PDB:6FNM
Method X-ray diffraction Resolution 1.16 Å Mutation Yes [1]
PDB Sequence
KEIDVSYVKI
617
EEVIGAGEFG
627
EVCRGRLKAP
637
GKKESCVAIK
647
TLKGGYTERQ
657

RREFLSEASI
667
MGQFEHPNII
677
RLEGVVTNSM
687
PVMILTEFME
697
NGALDSFLRL
707

NDGQFTVIQL
717
VGMLRGIASG
727
MRYLAEMSYV
737
HRDLAARNIL
747
VNSNLVCKVS
757

DFGLSRFLEE
767
GKIPIRWTAP
789
EAIAFRKFTS
799
ASDVWSYGIV
809
MWEVMSFGER
819

PYWDMSNQDV
829
INAIEQDYRL
839
PPPPDCPTSL
849
HQLMLDCWQK
859
DRNARPRFPQ
869

IVSALDKMIR
879
NPASLKIVAR
889
Residue
Distance (Å)
ILE621
3.594
GLY622
4.068
VAL629
3.958
ALA645
3.229
ILE646
3.631
LYS647
3.562
GLU664
3.357
MET668
3.800
ILE677
4.193
ILE691
3.436
LEU692
4.424
Residue
Distance (Å)
THR693
2.901
GLU694
3.584
PHE695
3.721
MET696
2.776
GLU697
2.999
ASN698
3.987
GLY699
3.497
LEU747
3.783
SER757
3.898
ASP758
4.902
Ligand Name: Staurosporine Ligand Info
Structure Description ephB4 kinase domain inhibitor complex PDB:2YN8
Method X-ray diffraction Resolution 2.11 Å Mutation Yes [2]
PDB Sequence
KEIDVSYVKI
617
EEVIGAGEFG
627
EVCRGRLKES
642
CVAIKTLKGG
652
YTERQRREFL
662

SEASIMGQFE
672
HPNIIRLEGV
682
VTNSMPVMIL
692
TEFMENGALD
702
SFLRLNDGQF
712

TVIQLVGMLR
722
GIASGMRYLA
732
EMSYVHRDLA
742
ARNILVNSNL
752
VCKVSDFPIR
785

WTAPEAIAFR
795
KFTSASDVWS
805
YGIVMWEVMS
815
FGERPYWDMS
825
NQDVINAIEQ
835

DYRLPPPPDC
845
PTSLHQLMLD
855
CWQKDRNARP
865
RFPQIVSALD
875
KMIRNPASLK
885

IVA
Residue
Distance (Å)
ILE621
3.490
GLY622
3.639
ALA623
3.437
GLY624
4.940
VAL629
3.806
ALA645
3.246
LYS647
3.236
GLU664
3.396
ILE677
4.182
THR693
3.191
GLU694
2.863
Residue
Distance (Å)
PHE695
3.410
MET696
2.731
GLU697
4.785
GLY699
3.518
ALA700
3.736
ARG744
2.869
ASN745
3.929
LEU747
3.361
SER757
3.034
ASP758
3.643
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: Phosphonotyrosine Ligand Info
Structure Description Crystal structure of EphB4 in complex with staurosporine PDB:3ZEW
Method X-ray diffraction Resolution 2.50 Å Mutation No [3]
PDB Sequence
EIDVSYVKIE
618
EVIGAGEFGE
628
VCRGRLKAPG
638
KKESCVAIKT
648
LTERQRREFL
662

SEASIMGQFE
672
HPNIIRLEGV
682
VTNSMPVMIL
692
TEFMENGALD
702
SFLRLNDGQF
712

TVIQLVGMLR
722
GIASGMRYLA
732
EMSYVHRDLA
742
ARNILVNSNL
752
VCKVSDFGLS
762

RFLSSDPTTS
776
SKIPIRWTAP
789
EAIAFRKFTS
799
ASDAWSYGIV
809
MWEVMSFGER
819

PYWDMSNQDV
829
INAIEQDYRL
839
PPPPDCPTSL
849
HQLMLDCWQK
859
DRNARPRFPQ
869

VVSALDKMIR
879
NPASLKIVA
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PTR or .PTR2 or .PTR3 or :3PTR;style chemicals stick;color identity;select .A:739 or .A:763 or .A:772 or .A:773 or .A:775 or .A:776 or .A:777 or .A:795 or .A:796 or .A:797; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG739
3.389
ARG763
3.323
PRO772
4.546
THR773
1.346
THR775
1.341
Residue
Distance (Å)
SER776
3.335
SER777
2.992
ARG795
3.005
LYS796
3.977
PHE797
2.827
Ligand Name: 3-({4-[(5-Chloro-1,3-benzodioxol-4-YL)amino]pyrimidin-2-YL}amino)benzamide Ligand Info
Structure Description ephB4 kinase domain inhibitor complex PDB:2VX1
Method X-ray diffraction Resolution 1.65 Å Mutation Yes [4]
PDB Sequence
KEIDVSYVKI
617
EEVIGAGEFG
627
EVCRGRLKAP
637
GKKESCVAIK
647
TLKGGYTERQ
657

RREFLSEASI
667
MGQFEHPNII
677
RLEGVVTNSM
687
PVMILTEFME
697
NGALDSFLRL
707

NDGQFTVIQL
717
VGMLRGIASG
727
MRYLAEMSYV
737
HRDLAARNIL
747
VNSNLVCKVS
757

DFGLSRFLEE
767
NSSDGGKIPI
784
RWTAPEAIAF
794
RKFTSASDAW
804
SYGIVMWEVM
814

SFGERPYWDM
824
SNQDVINAIE
834
QDYRLPPPPD
844
CPTSLHQLML
854
DCWQKDRNAR
864

PRFPQVVSAL
874
DKMIRNPASL
884
KIVA
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7X8 or .7X82 or .7X83 or :37X8;style chemicals stick;color identity;select .A:621 or .A:622 or .A:623 or .A:629 or .A:645 or .A:646 or .A:647 or .A:664 or .A:668 or .A:677 or .A:691 or .A:692 or .A:693 or .A:694 or .A:695 or .A:696 or .A:697 or .A:698 or .A:699 or .A:747 or .A:757 or .A:758; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE621
3.597
GLY622
3.624
ALA623
4.605
VAL629
3.878
ALA645
3.240
ILE646
3.835
LYS647
3.597
GLU664
3.506
MET668
4.154
ILE677
3.731
ILE691
3.504
Residue
Distance (Å)
LEU692
4.608
THR693
3.336
GLU694
3.189
PHE695
3.917
MET696
2.897
GLU697
4.132
ASN698
4.707
GLY699
3.498
LEU747
3.531
SER757
3.739
ASP758
4.933
Ligand Name: 3-({4-[(5-Chloro-1,3-benzodioxol-4-yl)amino]pyrimidin-2-yl}amino)benzenesulfonamide Ligand Info
Structure Description ephB4 kinase domain inhibitor complex PDB:2VWX
Method X-ray diffraction Resolution 1.65 Å Mutation Yes [4]
PDB Sequence
KEIDVSYVKI
617
EEVIGAGEFG
627
EVCRGRLKAP
637
GKKESCVAIK
647
TLKGGYTERQ
657

RREFLSEASI
667
MGQFEHPNII
677
RLEGVVTNSM
687
PVMILTEFME
697
NGALDSFLRL
707

NDGQFTVIQL
717
VGMLRGIASG
727
MRYLAEMSYV
737
HRDLAARNIL
747
VNSNLVCKVS
757

DFGLSRFLEE
767
NSSDGGKIPI
784
RWTAPEAIAF
794
RKFTSASDAW
804
SYGIVMWEVM
814

SFGERPYWDM
824
SNQDVINAIE
834
QDYRLPPPPD
844
CPTSLHQLML
854
DCWQKDRNAR
864

PRFPQVVSAL
874
DKMIRNPASL
884
KIVA
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7X4 or .7X42 or .7X43 or :37X4;style chemicals stick;color identity;select .A:621 or .A:622 or .A:629 or .A:645 or .A:646 or .A:647 or .A:664 or .A:668 or .A:677 or .A:691 or .A:692 or .A:693 or .A:694 or .A:695 or .A:696 or .A:697 or .A:698 or .A:699 or .A:747 or .A:757; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE621
3.473
GLY622
4.872
VAL629
4.026
ALA645
3.272
ILE646
3.775
LYS647
3.537
GLU664
3.426
MET668
4.033
ILE677
4.894
ILE691
3.510
Residue
Distance (Å)
LEU692
4.610
THR693
3.273
GLU694
3.164
PHE695
3.620
MET696
2.873
GLU697
2.677
ASN698
3.521
GLY699
3.578
LEU747
3.616
SER757
3.678
Ligand Name: N'-(5-chloro-1,3-benzodioxol-4-yl)-N-(3-methylsulfonylphenyl)pyrimidine-2,4-diamine Ligand Info
Structure Description ephB4 kinase domain inhibitor complex PDB:2VWY
Method X-ray diffraction Resolution 1.65 Å Mutation Yes [4]
PDB Sequence
KEIDVSYVKI
617
EEVIGAGEFG
627
EVCRGRLKAP
637
GKKESCVAIK
647
TLKGGYTERQ
657

RREFLSEASI
667
MGQFEHPNII
677
RLEGVVTNSM
687
PVMILTEFME
697
NGALDSFLRL
707

NDGQFTVIQL
717
VGMLRGIASG
727
MRYLAEMSYV
737
HRDLAARNIL
747
VNSNLVCKVS
757

DFGLSRFLEE
767
NSSDGGKIPI
784
RWTAPEAIAF
794
RKFTSASDAW
804
SYGIVMWEVM
814

SFGERPYWDM
824
SNQDVINAIE
834
QDYRLPPPPD
844
CPTSLHQLML
854
DCWQKDRNAR
864

PRFPQVVSAL
874
DKMIRNPASL
884
KIVA
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7X5 or .7X52 or .7X53 or :37X5;style chemicals stick;color identity;select .A:621 or .A:622 or .A:629 or .A:645 or .A:646 or .A:647 or .A:664 or .A:668 or .A:677 or .A:691 or .A:692 or .A:693 or .A:694 or .A:695 or .A:696 or .A:697 or .A:698 or .A:699 or .A:747 or .A:757 or .A:758; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE621
3.422
GLY622
4.809
VAL629
4.011
ALA645
3.239
ILE646
3.866
LYS647
3.572
GLU664
3.549
MET668
4.152
ILE677
3.590
ILE691
3.408
LEU692
4.629
Residue
Distance (Å)
THR693
3.419
GLU694
3.203
PHE695
3.738
MET696
2.926
GLU697
2.984
ASN698
3.643
GLY699
3.643
LEU747
3.593
SER757
3.587
ASP758
4.862
Ligand Name: N-(2-Methoxyethyl)-4-[(6-Pyridin-4-Ylquinazolin-2-Yl)amino]benzamide Ligand Info
Structure Description ephB4 kinase domain inhibitor complex PDB:4BB4
Method X-ray diffraction Resolution 1.65 Å Mutation Yes [5]
PDB Sequence
FAKEIDVSYV
615
KIEEVIGAGE
625
FGEVCRGRLK
635
APGKKESCVA
645
IKTLYTERQR
658

REFLSEASIM
668
GQFEHPNIIR
678
LEGVVTNSMP
688
VMILTEFMEN
698
GALDSFLRLN
708

DGQFTVIQLV
718
GMLRGIASGM
728
RYLAEMSYVH
738
RDLAARNILV
748
NSNLVCKVSD
758

FGLSRFGKIP
783
IRWTAPEAIA
793
FRKFTSASDA
803
WSYGIVMWEV
813
MSFGERPYWD
823

MSNQDVINAI
833
EQDYRLPPPP
843
DCPTSLHQLM
853
LDCWQKDRNA
863
RPRFPQVVSA
873

LDKMIRNPAS
883
LKIVA
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .32W or .32W2 or .32W3 or :332W;style chemicals stick;color identity;select .A:619 or .A:620 or .A:621 or .A:622 or .A:629 or .A:645 or .A:647 or .A:664 or .A:668 or .A:691 or .A:693 or .A:694 or .A:695 or .A:696 or .A:697 or .A:698 or .A:699 or .A:747 or .A:757 or .A:758; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLU619
3.731
VAL620
3.454
ILE621
2.708
GLY622
4.907
VAL629
3.628
ALA645
3.274
LYS647
3.553
GLU664
3.163
MET668
3.629
ILE691
3.742
Residue
Distance (Å)
THR693
3.300
GLU694
3.647
PHE695
3.685
MET696
2.697
GLU697
3.506
ASN698
4.396
GLY699
3.455
LEU747
3.563
SER757
3.299
ASP758
4.887
Ligand Name: N-[3-[[4-[(5-Chloro-1,3-benzodioxol-4-YL)amino]pyrimidin-2-YL]amino]phenyl]methanesulfonamide Ligand Info
Structure Description ephB4 kinase domain inhibitor complex PDB:2VWZ
Method X-ray diffraction Resolution 1.65 Å Mutation Yes [4]
PDB Sequence
KEIDVSYVKI
617
EEVIGAGEFG
627
EVCRGRLKAP
637
GKKESCVAIK
647
TLKGGYTERQ
657

RREFLSEASI
667
MGQFEHPNII
677
RLEGVVTNSM
687
PVMILTEFME
697
NGALDSFLRL
707

NDGQFTVIQL
717
VGMLRGIASG
727
MRYLAEMSYV
737
HRDLAARNIL
747
VNSNLVCKVS
757

DFGLSRFLEE
767
NSSDGGKIPI
784
RWTAPEAIAF
794
RKFTSASDAW
804
SYGIVMWEVM
814

SFGERPYWDM
824
SNQDVINAIE
834
QDYRLPPPPD
844
CPTSLHQLML
854
DCWQKDRNAR
864

PRFPQVVSAL
874
DKMIRNPASL
884
KIVA
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7X6 or .7X62 or .7X63 or :37X6;style chemicals stick;color identity;select .A:621 or .A:622 or .A:623 or .A:629 or .A:645 or .A:646 or .A:647 or .A:664 or .A:668 or .A:677 or .A:691 or .A:692 or .A:693 or .A:694 or .A:695 or .A:696 or .A:697 or .A:698 or .A:699 or .A:700 or .A:747 or .A:757; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE621
3.566
GLY622
3.950
ALA623
4.046
VAL629
3.731
ALA645
3.268
ILE646
3.870
LYS647
3.578
GLU664
3.493
MET668
4.122
ILE677
3.665
ILE691
3.407
Residue
Distance (Å)
LEU692
4.642
THR693
3.424
GLU694
3.188
PHE695
3.838
MET696
2.905
GLU697
3.948
ASN698
4.641
GLY699
3.505
ALA700
4.122
LEU747
3.465
SER757
3.709
Ligand Name: {4-Methyl-3-[(1-methylethyl)(2-{[3-(methylsulfonyl)-5-morpholin-4-ylphenyl]amino}pyrimidin-4-YL)amino]phenyl}methanol Ligand Info
Structure Description ephB4 kinase domain inhibitor complex PDB:2XVD
Method X-ray diffraction Resolution 1.70 Å Mutation Yes [6]
PDB Sequence
AKEIDVSYVK
616
IEEVIGAGEF
626
GEVCRGRLKA
636
PGKKESCVAI
646
KTLYTERQRR
659

EFLSEASIMG
669
QFEHPNIIRL
679
EGVVTNSMPV
689
MILTEFMENG
699
ALDSFLRLND
709

GQFTVIQLVG
719
MLRGIASGMR
729
YLAEMSYVHR
739
DLAARNILVN
749
SNLVCKVSDF
759

GLSRFLESSL
778
GGKIPIRWTA
788
PEAIAFRKFT
798
SASDAWSYGI
808
VMWEVMSFGE
818

RPYWDMSNQD
828
VINAIEQDYR
838
LPPPPDCPTS
848
LHQLMLDCWQ
858
KDRNARPRFP
868

QVVSALDKMI
878
RNPASLKIVA
888
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .AS6 or .AS62 or .AS63 or :3AS6;style chemicals stick;color identity;select .A:621 or .A:622 or .A:623 or .A:629 or .A:645 or .A:646 or .A:647 or .A:664 or .A:668 or .A:677 or .A:691 or .A:693 or .A:694 or .A:695 or .A:696 or .A:697 or .A:698 or .A:699 or .A:700 or .A:747 or .A:757 or .A:758 or .A:759; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE621
3.568
GLY622
3.610
ALA623
4.934
VAL629
3.385
ALA645
3.388
ILE646
3.721
LYS647
3.830
GLU664
2.794
MET668
3.574
ILE677
4.412
ILE691
4.237
THR693
3.099
Residue
Distance (Å)
GLU694
2.997
PHE695
3.929
MET696
2.945
GLU697
3.164
ASN698
4.630
GLY699
3.524
ALA700
4.174
LEU747
3.452
SER757
3.429
ASP758
2.861
PHE759
4.063
Ligand Name: N^4^-1H-Indazol-4-YL-N^2^-[3-(methylsulfonyl)phenyl]pyrimidine-2,4-diamine Ligand Info
Structure Description ephB4 kinase domain inhibitor complex PDB:2X9F
Method X-ray diffraction Resolution 1.75 Å Mutation Yes [7]
PDB Sequence
KEIDVSYVKI
617
EEVIGAGEFG
627
EVCRGRLKAP
637
GKKESCVAIK
647
TLYTERQRRE
660

FLSEASIMGQ
670
FEHPNIIRLE
680
GVVTNSMPVM
690
ILTEFMENGA
700
LDSFLRLNDG
710

QFTVIQLVGM
720
LRGIASGMRY
730
LAEMSYVHRD
740
LAARNILVNS
750
NLVCKVSDFG
760

LSRFLGGKIP
783
IRWTAPEAIA
793
FRKFTSASDA
803
WSYGIVMWEV
813
MSFGERPYWD
823

MSNQDVINAI
833
EQDYRLPPPP
843
DCPTSLHQLM
853
LDCWQKDRNA
863
RPRFPQVVSA
873

LDKMIRNPAS
883
LKIVA
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .X9F or .X9F2 or .X9F3 or :3X9F;style chemicals stick;color identity;select .A:621 or .A:629 or .A:645 or .A:646 or .A:647 or .A:664 or .A:668 or .A:677 or .A:691 or .A:693 or .A:694 or .A:695 or .A:696 or .A:697 or .A:698 or .A:699 or .A:747 or .A:757 or .A:758 or .A:759; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE621
3.523
VAL629
3.763
ALA645
3.202
ILE646
4.469
LYS647
3.518
GLU664
2.667
MET668
4.199
ILE677
3.862
ILE691
4.034
THR693
3.272
Residue
Distance (Å)
GLU694
3.077
PHE695
3.406
MET696
2.825
GLU697
3.215
ASN698
3.824
GLY699
3.520
LEU747
3.488
SER757
3.463
ASP758
3.055
PHE759
4.897
Ligand Name: N'-(3-Chloro-4-Methoxy-Phenyl)-N-(3,4,5-Trimethoxyphenyl)-1,3,5-Triazine-2,4-Diamine Ligand Info
Structure Description ephB4 kinase domain inhibitor complex PDB:2VWV
Method X-ray diffraction Resolution 1.90 Å Mutation Yes [8]
PDB Sequence
FAKEIDVSYV
615
KIEEVIGAGE
625
FGEVCRGRLK
635
APGKKESCVA
645
IKTLTERQRR
659

EFLSEASIMG
669
QFEHPNIIRL
679
EGVVTNSMPV
689
MILTEFMENG
699
ALDSFLRLND
709

GQFTVIQLVG
719
MLRGIASGMR
729
YLAEMSYVHR
739
DLAARNILVN
749
SNLVCKVSDF
759

KIPIRWTAPE
790
AIAFRKFTSA
800
SDAWSYGIVM
810
WEVMSFGERP
820
YWDMSNQDVI
830

NAIEQDYRLP
840
PPPDCPTSLH
850
QLMLDCWQKD
860
RNARPRFPQV
870
VSALDKMIRN
880

PASLK
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7X3 or .7X32 or .7X33 or :37X3;style chemicals stick;color identity;select .A:621 or .A:622 or .A:623 or .A:624 or .A:629 or .A:645 or .A:647 or .A:677 or .A:693 or .A:694 or .A:695 or .A:696 or .A:697 or .A:699 or .A:700 or .A:747; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE621
3.237
GLY622
3.689
ALA623
3.233
GLY624
4.112
VAL629
3.548
ALA645
3.377
LYS647
3.611
ILE677
4.037
Residue
Distance (Å)
THR693
3.118
GLU694
3.207
PHE695
3.904
MET696
2.921
GLU697
3.643
GLY699
3.674
ALA700
4.081
LEU747
3.475
Ligand Name: N'-(5-Chloro-1,3-benzodioxol-4-YL)-N-(3,4,5-trimethoxyphenyl)pyrimidine-2,4-diamine Ligand Info
Structure Description ephB4 kinase domain inhibitor complex PDB:2VWW
Method X-ray diffraction Resolution 1.90 Å Mutation Yes [8]
PDB Sequence
EIDVSYVKIE
618
EVIGAGEFGE
628
VCRGRLKAPG
638
KKESCVAIKT
648
LTERQRREFL
662

SEASIMGQFE
672
HPNIIRLEGV
682
VTNSMPVMIL
692
TEFMENGALD
702
SFLRLNDGQF
712

TVIQLVGMLR
722
GIASGMRYLA
732
EMSYVHRDLA
742
ARNILVNSNL
752
VCKVSDFIPI
784

RWTAPEAIAF
794
RKFTSASDAW
804
SYGIVMWEVM
814
SFGERPYWDM
824
SNQDVINAIE
834

QDYRLPPPPD
844
CPTSLHQLML
854
DCWQKDRNAR
864
PRFPQVVSAL
874
DKMIRNPASL
884

KIV
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7X2 or .7X22 or .7X23 or :37X2;style chemicals stick;color identity;select .A:621 or .A:622 or .A:629 or .A:645 or .A:646 or .A:647 or .A:664 or .A:668 or .A:677 or .A:691 or .A:692 or .A:693 or .A:694 or .A:695 or .A:696 or .A:697 or .A:698 or .A:699 or .A:700 or .A:747 or .A:757 or .A:758; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE621
3.333
GLY622
4.493
VAL629
3.856
ALA645
3.236
ILE646
3.862
LYS647
3.605
GLU664
3.568
MET668
4.245
ILE677
3.536
ILE691
3.518
LEU692
4.629
Residue
Distance (Å)
THR693
3.411
GLU694
3.111
PHE695
3.634
MET696
2.838
GLU697
3.279
ASN698
4.776
GLY699
3.564
ALA700
3.622
LEU747
3.445
SER757
3.542
ASP758
4.956
Ligand Name: N-(5-chloro-1,3-benzodioxol-4-yl)-6-methoxy-7-(3-piperidin-1-ylpropoxy)quinazolin-4-amine Ligand Info
Structure Description ephB4 kinase domain inhibitor complex PDB:2VWU
Method X-ray diffraction Resolution 2.00 Å Mutation Yes [8]
PDB Sequence
EIDVSYVKIE
618
EVIGAGEFGE
628
VCRGRLKAPG
638
KKESCVAIKT
648
LTERQRREFL
662

SEASIMGQFE
672
HPNIIRLEGV
682
VTNSMPVMIL
692
TEFMENGALD
702
SFLRLNDGQF
712

TVIQLVGMLR
722
GIASGMRYLA
732
EMSYVHRDLA
742
ARNILVNSNL
752
VCKVSDFIPI
784

RWTAPEAIAF
794
RKFTSASDAW
804
SYGIVMWEVM
814
SFGERPYWDM
824
SNQDVINAIE
834

QDYRLPPPPD
844
CPTSLHQLML
854
DCWQKDRNAR
864
PRFPQVVSAL
874
DKMIRNPASL
884

KIV
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7X1 or .7X12 or .7X13 or :37X1;style chemicals stick;color identity;select .A:621 or .A:622 or .A:629 or .A:645 or .A:646 or .A:647 or .A:664 or .A:668 or .A:677 or .A:691 or .A:692 or .A:693 or .A:694 or .A:695 or .A:696 or .A:697 or .A:698 or .A:699 or .A:707 or .A:747 or .A:757 or .A:758; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE621
3.445
GLY622
4.399
VAL629
3.972
ALA645
3.223
ILE646
3.862
LYS647
3.580
GLU664
3.566
MET668
3.794
ILE677
3.667
ILE691
3.332
LEU692
4.490
Residue
Distance (Å)
THR693
3.038
GLU694
3.186
PHE695
3.912
MET696
3.032
GLU697
3.413
ASN698
3.949
GLY699
3.621
LEU707
4.757
LEU747
3.375
SER757
3.429
ASP758
4.604
Ligand Name: N'-(5-Chloro-1,3-Benzodioxol-4-Yl)-N-(3-Morpholin-4-Ylphenyl)pyrimidine-2,4-Diamine Ligand Info
Structure Description ephB4 kinase domain inhibitor complex PDB:2VX0
Method X-ray diffraction Resolution 2.10 Å Mutation Yes [8]
PDB Sequence
KEIDVSYVKI
617
EEVIGAGEFG
627
EVCRGRLKAP
637
GKKESCVAIK
647
TLKGGYTERQ
657

RREFLSEASI
667
MGQFEHPNII
677
RLEGVVTNSM
687
PVMILTEFME
697
NGALDSFLRL
707

NDGQFTVIQL
717
VGMLRGIASG
727
MRYLAEMSYV
737
HRDLAARNIL
747
VNSNLVCKVS
757

DFGLSRFLEE
767
NSSDGKIPIR
785
WTAPEAIAFR
795
KFTSASDAWS
805
YGIVMWEVMS
815

FGERPYWDMS
825
NQDVINAIEQ
835
DYRLPPPPDC
845
PTSLHQLMLD
855
CWQKDRNARP
865

RFPQVVSALD
875
KMIRNPASLK
885
IVA
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7X7 or .7X72 or .7X73 or :37X7;style chemicals stick;color identity;select .A:621 or .A:622 or .A:629 or .A:645 or .A:646 or .A:647 or .A:664 or .A:668 or .A:677 or .A:691 or .A:692 or .A:693 or .A:694 or .A:695 or .A:696 or .A:697 or .A:698 or .A:699 or .A:747 or .A:757 or .A:758; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE621
3.536
GLY622
4.851
VAL629
4.104
ALA645
3.238
ILE646
3.779
LYS647
3.520
GLU664
3.393
MET668
4.126
ILE677
3.750
ILE691
3.458
LEU692
4.711
Residue
Distance (Å)
THR693
3.330
GLU694
3.185
PHE695
3.754
MET696
2.868
GLU697
2.970
ASN698
3.898
GLY699
3.486
LEU747
3.630
SER757
3.612
ASP758
4.916
Ligand Name: 1-Methyl-6-pyridin-3-yl-pyrazolo[3,4-d]pyrimidin-4-amine Ligand Info
Structure Description Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with a pyrazolo[3,4-d]pyrimidine fragment of NVP-BHG712 PDB:6FNK
Method X-ray diffraction Resolution 1.05 Å Mutation Yes [1]
PDB Sequence
REFAKEIDVS
613
YVKIEEVIGA
623
GEFGEVCRGR
633
LKAPGKKESC
643
VAIKTLKGGY
653

TERQRREFLS
663
EASIMGQFEH
673
PNIIRLEGVV
683
TNSMPVMILT
693
EFMENGALDS
703

FLRLNDGQFT
713
VIQLVGMLRG
723
IASGMRYLAE
733
MSYVHRDLAA
743
RNILVNSNLV
753

CKVSDFGLSR
763
FLEEGKIPIR
785
WTAPEAIAFR
795
KFTSASDVWS
805
YGIVMWEVMS
815

FGERPYWDMS
825
NQDVINAIEQ
835
DYRLPPPPDC
845
PTSLHQLMLD
855
CWQKDRNARP
865

RFPQIVSALD
875
KMIRNPASLK
885
IVAR
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DXK or .DXK2 or .DXK3 or :3DXK;style chemicals stick;color identity;select .A:621 or .A:622 or .A:623 or .A:624 or .A:629 or .A:645 or .A:647 or .A:677 or .A:693 or .A:694 or .A:695 or .A:696 or .A:699 or .A:747; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE621
3.782
GLY622
4.408
ALA623
3.119
GLY624
3.616
VAL629
3.722
ALA645
3.183
LYS647
3.732
Residue
Distance (Å)
ILE677
4.463
THR693
2.882
GLU694
3.327
PHE695
3.866
MET696
2.954
GLY699
4.308
LEU747
3.663
Ligand Name: NVP-BHG712 isomer Ligand Info
Structure Description Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with an isomer of NVP-BHG712 PDB:6FNJ
Method X-ray diffraction Resolution 1.24 Å Mutation Yes [1]
PDB Sequence
AKEIDVSYVK
616
IEEVIGAGEF
626
GEVCRGRLKA
636
PGKKESCVAI
646
KTLKGGYTER
656

QRREFLSEAS
666
IMGQFEHPNI
676
IRLEGVVTNS
686
MPVMILTEFM
696
ENGALDSFLR
706

LNDGQFTVIQ
716
LVGMLRGIAS
726
GMRYLAEMSY
736
VHRDLAARNI
746
LVNSNLVCKV
756

SDFGLIPIRW
786
TAPEAIAFRK
796
FTSASDVWSY
806
GIVMWEVMSF
816
GERPYWDMSN
826

QDVINAIEQD
836
YRLPPPPDCP
846
TSLHQLMLDC
856
WQKDRNARPR
866
FPQIVSALDK
876

MIRNPASLKI
886
VA
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DWT or .DWT2 or .DWT3 or :3DWT;style chemicals stick;color identity;select .A:621 or .A:629 or .A:645 or .A:646 or .A:647 or .A:664 or .A:667 or .A:668 or .A:671 or .A:676 or .A:677 or .A:691 or .A:692 or .A:693 or .A:694 or .A:695 or .A:696 or .A:699 or .A:731 or .A:736 or .A:738 or .A:747 or .A:756 or .A:757 or .A:758 or .A:759; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE621
4.082
VAL629
3.648
ALA645
3.253
ILE646
4.029
LYS647
3.608
GLU664
2.978
ILE667
4.536
MET668
3.337
PHE671
3.366
ILE676
3.607
ILE677
3.497
ILE691
3.765
LEU692
4.879
Residue
Distance (Å)
THR693
2.989
GLU694
4.433
PHE695
3.484
MET696
3.015
GLY699
3.932
LEU731
3.843
TYR736
3.394
HIS738
3.613
LEU747
3.598
VAL756
3.615
SER757
3.145
ASP758
2.887
PHE759
3.331
Ligand Name: 4-methyl-3-(1-methyl-6-(pyridin-3-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-ylamino)-N-(3-(trifluoromethyl)phenyl)benzamide Ligand Info
Structure Description Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with NVP-BHG712 PDB:6FNI
Method X-ray diffraction Resolution 1.47 Å Mutation Yes [1]
PDB Sequence
AKEIDVSYVK
616
IEEVIGAGEF
626
GEVCRGRLKA
636
PGKKESCVAI
646
KTLERQRREF
661

LSEASIMGQF
671
EHPNIIRLEG
681
VVTNSMPVMI
691
LTEFMENGAL
701
DSFLRLNDGQ
711

FTVIQLVGML
721
RGIASGMRYL
731
AEMSYVHRDL
741
AARNILVNSN
751
LVCKVSDFGL
761

SRFIPIRWTA
788
PEAIAFRKFT
798
SASDVWSYGI
808
VMWEVMSFGE
818
RPYWDMSNQD
828

VINAIEQDYR
838
LPPPPDCPTS
848
LHQLMLDCWQ
858
KDRNARPRFP
868
QIVSALDKMI
878

RNPASLKIVA
888
R
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DXH or .DXH2 or .DXH3 or :3DXH;style chemicals stick;color identity;select .A:621 or .A:622 or .A:623 or .A:629 or .A:645 or .A:646 or .A:647 or .A:664 or .A:667 or .A:668 or .A:671 or .A:676 or .A:677 or .A:691 or .A:693 or .A:694 or .A:695 or .A:696 or .A:699 or .A:731 or .A:736 or .A:738 or .A:747 or .A:756 or .A:757 or .A:758 or .A:759 or .A:762 or .A:763 or .A:764; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE621
3.772
GLY622
4.286
ALA623
3.823
VAL629
3.821
ALA645
3.411
ILE646
4.080
LYS647
3.869
GLU664
2.914
ILE667
4.072
MET668
3.281
PHE671
3.461
ILE676
3.458
ILE677
3.595
ILE691
4.207
THR693
2.897
Residue
Distance (Å)
GLU694
3.404
PHE695
3.746
MET696
3.081
GLY699
4.404
LEU731
3.861
TYR736
3.234
HIS738
3.523
LEU747
3.455
VAL756
3.579
SER757
2.940
ASP758
2.826
PHE759
3.439
SER762
3.553
ARG763
3.721
PHE764
3.476
Ligand Name: (3z)-5-[(1-Ethylpiperidin-4-Yl)amino]-3-[(5-Methoxy-1h-Benzimidazol-2-Yl)(Phenyl)methylidene]-1,3-Dihydro-2h-Indol-2-One Ligand Info
Structure Description Complex of the EphB4 kinase domain with an oxindole inhibitor PDB:4AW5
Method X-ray diffraction Resolution 2.33 Å Mutation No [9]
PDB Sequence
AKEIDVSYVK
92
IEEVIGAGEF
102
GEVCRGRLKA
112
PGKKESCVAI
122
KTLKGGYTER
132

QRREFLSEAS
142
IMGQFEHPNI
152
IRLEGVVTNS
162
MPVMILTEFM
172
ENGALDSFLR
182

LNDGQFTVIQ
192
LVGMLRGIAS
202
GMRYLAEMSY
212
VHRDLAARNI
222
LVNSNLVCKV
232

SDFGIPIRWT
263
APEAIAFRKF
273
TSASDAWSYG
283
IVMWEVMSFG
293
ERPYWDMSNQ
303

DVINAIEQDY
313
RLPPPPDCPT
323
SLHQLMLDCW
333
QKDRNARPRF
343
PQVVSALDKM
353

IRNPASLKIV
363
A
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .30K or .30K2 or .30K3 or :330K;style chemicals stick;color identity;select .A:97 or .A:98 or .A:99 or .A:100 or .A:105 or .A:121 or .A:123 or .A:153 or .A:169 or .A:170 or .A:171 or .A:172 or .A:173 or .A:174 or .A:175 or .A:176 or .A:220 or .A:221 or .A:223 or .A:233 or .A:234; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE97
3.541
GLY98
3.973
ALA99
4.012
GLY100
4.466
VAL105
3.829
ALA121
3.225
LYS123
3.456
ILE153
3.411
THR169
3.168
GLU170
3.227
PHE171
3.494
Residue
Distance (Å)
MET172
2.941
GLU173
3.351
ASN174
4.542
GLY175
3.575
ALA176
4.302
ARG220
3.625
ASN221
3.404
LEU223
3.589
SER233
3.701
ASP234
4.865
References  Top
REF 1 NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. ChemMedChem. 2018 Aug 20;13(16):1629-1633.
REF 2 Stability and solubility engineering of the EphB4 tyrosine kinase catalytic domain using a rationally designed synthetic library. Protein Eng Des Sel. 2013 Oct;26(10):695-704.
REF 3 Completing the structural family portrait of the human EphB tyrosine kinase domains. Protein Sci. 2014 May;23(5):627-38.
REF 4 Inhibitors of the tyrosine kinase EphB4. Part 2: structure-based discovery and optimisation of 3,5-bis substituted anilinopyrimidines. Bioorg Med Chem Lett. 2008 Nov 1;18(21):5717-21.
REF 5 Discovery and optimization of a novel series of potent mutant B-Raf(V600E) selective kinase inhibitors. J Med Chem. 2013 Mar 14;56(5):1996-2015.
REF 6 Inhibitors of the tyrosine kinase EphB4. Part 4: Discovery and optimization of a benzylic alcohol series. Bioorg Med Chem Lett. 2011 Apr 15;21(8):2207-11.
REF 7 Inhibitors of the tyrosine kinase EphB4. Part 3: identification of non-benzodioxole-based kinase inhibitors. Bioorg Med Chem Lett. 2010 Nov 1;20(21):6242-5
REF 8 Inhibitors of the tyrosine kinase EphB4. Part 1: Structure-based design and optimization of a series of 2,4-bis-anilinopyrimidines. Bioorg Med Chem Lett. 2008 May 1;18(9):2776-80.
REF 9 The design, synthesis, and biological evaluation of potent receptor tyrosine kinase inhibitors. Bioorg Med Chem Lett. 2012 Aug 1;22(15):4979-85.

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