Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T05876 Target Info
Target Name Ebola virus Envelope glycoprotein (EV GP)
Synonyms GP1,2; GP
Target Type Successful Target
Gene Name EV GP
UniProt ID
VGP_EBOZM
Drug Binding Sites of Target  Top
Ligand Name: Sertraline Ligand Info
Structure Description CRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH SERTRALINE PDB:6F6N
Method X-ray diffraction Resolution 2.15 Å Mutation Yes [1]
PDB Sequence
.
Residue
Distance (Å)
ILE38[A]
3.593
LEU43[A]
4.612
ARG64[A]
3.535
SER65[A]
4.129
VAL66[A]
3.420
ALA101[A]
3.595
LEU184[A]
3.992
LEU186[A]
3.445
Residue
Distance (Å)
LEU515[B]
4.360
TYR517[B]
3.307
THR519[B]
4.763
MET548[B]
3.511
LEU554[B]
3.772
ILE555[B]
4.089
LEU558[B]
3.474
Ligand Name: Clomipramine Ligand Info
Structure Description Crystal structure of Ebolavirus glycoprotein in complex with clomipramine PDB:6G9I
Method X-ray diffraction Resolution 2.19 Å Mutation Yes [2]
PDB Sequence
.
Residue
Distance (Å)
ILE38[A]
3.554
LEU43[A]
3.902
ARG64[A]
4.267
VAL66[A]
3.972
ALA101[A]
4.733
LEU184[A]
3.869
ILE185[A]
4.409
Residue
Distance (Å)
LEU186[A]
3.507
PRO187[A]
4.213
LEU515[B]
4.217
MET548[B]
3.445
LEU554[B]
4.194
ILE555[B]
4.421
LEU558[B]
3.597
Ligand Name: Imipramine Ligand Info
Structure Description Crystal structure of Ebolavirus glycoprotein in complex with imipramine PDB:6G9B
Method X-ray diffraction Resolution 2.26 Å Mutation Yes [2]
PDB Sequence
.
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .IXX or .IXX2 or .IXX3 or :3IXX;style chemicals stick;color identity;select .A:36 or .A:37 or .A:38 or .A:43 or .A:66 or .A:184 or .A:185 or .A:186 or .A:187 or .A:64 or .A:101 or .A:186 or .B:515 or .B:548 or .B:554 or .B:555 or .B:558 or .B:517 or .B:519 or .B:521 or .B:544 or .B:548; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY36[A]
4.499
VAL37[A]
4.870
ILE38[A]
3.434
LEU43[A]
3.500
VAL66[A]
3.940
LEU184[A]
3.559
ILE185[A]
3.677
LEU186[A]
3.535
PRO187[A]
4.038
ARG64[A]
3.053
ALA101[A]
3.764
Residue
Distance (Å)
LEU186[A]
4.040
LEU515[B]
3.750
MET548[B]
3.621
LEU554[B]
4.143
ILE555[B]
4.150
LEU558[B]
4.078
TYR517[B]
3.074
THR519[B]
4.593
GLN521[B]
3.195
ILE544[B]
3.581
MET548[B]
4.587
Ligand Name: Paroxetine Ligand Info
Structure Description CRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH PAROXETINE PDB:6F6I
Method X-ray diffraction Resolution 2.40 Å Mutation Yes [1]
PDB Sequence
.
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8PR or .8PR2 or .8PR3 or :38PR;style chemicals stick;color identity;select .A:64 or .A:65 or .A:66 or .A:67 or .A:68 or .A:100 or .A:101 or .A:102 or .A:103 or .A:184 or .A:186 or .B:515 or .B:517 or .B:518 or .B:519 or .B:548 or .B:558; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG64[A]
3.284
SER65[A]
4.637
VAL66[A]
3.278
GLY67[A]
3.288
LEU68[A]
3.542
GLU100[A]
3.525
ALA101[A]
3.475
GLY102[A]
3.359
GLU103[A]
4.299
Residue
Distance (Å)
LEU184[A]
4.223
LEU186[A]
3.907
LEU515[B]
3.489
TYR517[B]
3.547
TRP518[B]
4.995
THR519[B]
3.630
MET548[B]
3.483
LEU558[B]
3.911
Ligand Name: Ibuprofen Ligand Info
Structure Description Crystal structure of Ebola glycoprotein in complex with ibuprofen PDB:5JQB
Method X-ray diffraction Resolution 2.68 Å Mutation Yes [3]
PDB Sequence
.
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .IBP or .IBP2 or .IBP3 or :3IBP;style chemicals stick;color identity;select .A:38 or .A:43 or .A:64 or .A:66 or .A:101 or .A:184 or .A:186 or .B:515 or .B:517 or .B:519 or .B:548 or .B:554 or .B:558; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE38[A]
4.678
LEU43[A]
4.602
ARG64[A]
2.979
VAL66[A]
4.265
ALA101[A]
3.599
LEU184[A]
3.700
LEU186[A]
3.841
Residue
Distance (Å)
LEU515[B]
3.988
TYR517[B]
3.306
THR519[B]
4.298
MET548[B]
3.363
LEU554[B]
4.337
LEU558[B]
3.961
Ligand Name: Toremifene Ligand Info
Structure Description Crystal structure of Ebola glycoprotein in complex with toremifene PDB:5JQ7
Method X-ray diffraction Resolution 2.69 Å Mutation Yes [3]
PDB Sequence
.
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .T0R or .T0R2 or .T0R3 or :3T0R;style chemicals stick;color identity;select .A:64 or .A:66 or .A:67 or .A:68 or .A:100 or .A:101 or .A:102 or .A:103 or .A:184 or .A:186 or .B:515 or .B:517 or .B:519 or .B:520 or .B:521 or .B:522 or .B:548 or .B:554 or .B:558; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG64[A]
3.585
VAL66[A]
3.216
GLY67[A]
4.291
LEU68[A]
3.975
GLU100[A]
3.560
ALA101[A]
3.592
GLY102[A]
3.746
GLU103[A]
4.915
LEU184[A]
3.660
LEU186[A]
3.712
Residue
Distance (Å)
LEU515[B]
3.272
TYR517[B]
3.456
THR519[B]
3.383
THR520[B]
3.299
GLN521[B]
4.330
ASP522[B]
3.810
MET548[B]
3.815
LEU554[B]
4.471
LEU558[B]
3.726
Ligand Name: Benztropine Ligand Info
Structure Description CRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH benztropine PDB:6F6S
Method X-ray diffraction Resolution 2.29 Å Mutation Yes [1]
PDB Sequence
.
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CXQ or .CXQ2 or .CXQ3 or :3CXQ;style chemicals stick;color identity;select .A:64 or .A:101 or .A:186 or .A:38 or .A:43 or .A:66 or .A:101 or .A:184 or .A:186 or .A:187 or .B:517 or .B:519 or .B:521 or .B:544 or .B:515 or .B:517 or .B:548 or .B:554 or .B:555 or .B:558; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG64[A]
3.052
ALA101[A]
3.678
LEU186[A]
4.462
ILE38[A]
4.031
LEU43[A]
4.327
VAL66[A]
3.604
ALA101[A]
4.670
LEU184[A]
3.717
LEU186[A]
3.539
PRO187[A]
4.326
Residue
Distance (Å)
TYR517[B]
3.150
THR519[B]
4.135
GLN521[B]
3.667
ILE544[B]
3.487
LEU515[B]
4.002
TYR517[B]
3.773
MET548[B]
3.136
LEU554[B]
3.591
ILE555[B]
4.381
LEU558[B]
4.545
Ligand Name: Alpha-D-Mannose Ligand Info
Structure Description EM structure of a EBOV-GP bound to 3T0331 neutralizing antibody PDB:6QD7
Method Electron microscopy Resolution 3.10 Å Mutation No [4]
PDB Sequence
.
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MAN or .MAN2 or .MAN3 or :3MAN;style chemicals stick;color identity;select .A:84 or .A:155 or .A:156; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS84
4.642
LYS155
3.811
Residue
Distance (Å)
GLU156
4.344
Ligand Name: 1-(2-(3-hydroxy-4-(4-phenyl-1H-pyrazol-3-yl)phenoxy)ethyl)piperidine-4-carboxamide Ligand Info
Structure Description Crystal structure of Ebolavirus glycoprotein in complex with inhibitor 118 PDB:6HS4
Method X-ray diffraction Resolution 2.05 Å Mutation Yes [5]
PDB Sequence
.
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GON or .GON2 or .GON3 or :3GON;style chemicals stick;color identity;select .A:38 or .A:43 or .A:60 or .A:61 or .A:63 or .A:64 or .A:65 or .A:66 or .A:68 or .A:100 or .A:101 or .A:102 or .A:184 or .A:186 or .A:187 or .A:189 or .B:515 or .B:517 or .B:519 or .B:520 or .B:522 or .B:548 or .B:554 or .B:555 or .B:558; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE38[A]
3.876
LEU43[A]
4.185
THR60[A]
4.412
ASN61[A]
3.230
LEU63[A]
4.959
ARG64[A]
3.506
SER65[A]
4.928
VAL66[A]
3.494
LEU68[A]
4.940
GLU100[A]
3.315
ALA101[A]
3.671
GLY102[A]
4.473
LEU184[A]
4.130
Residue
Distance (Å)
LEU186[A]
3.565
PRO187[A]
3.526
ALA189[A]
3.382
LEU515[B]
3.252
TYR517[B]
3.510
THR519[B]
3.268
THR520[B]
3.798
ASP522[B]
3.118
MET548[B]
2.927
LEU554[B]
3.698
ILE555[B]
4.592
LEU558[B]
3.499
Ligand Name: 1-[2-[4-[4-(4-chlorophenyl)-3-methyl-1~{H}-pyrazol-5-yl]-3-oxidanyl-phenoxy]ethyl]piperidin-1-ium-4-carboxamide Ligand Info
Structure Description Crystal structure of Ebolavirus glycoprotein in complex with inhibitor 118a PDB:6HRO
Method X-ray diffraction Resolution 2.30 Å Mutation Yes [5]
PDB Sequence
.
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GKZ or .GKZ2 or .GKZ3 or :3GKZ;style chemicals stick;color identity;select .A:38 or .A:43 or .A:64 or .A:184 or .A:186 or .A:187 or .A:189 or .A:190 or .A:191 or .A:60 or .A:61 or .A:63 or .A:64 or .A:66 or .A:67 or .A:68 or .A:100 or .A:101 or .A:102 or .A:103 or .B:548 or .B:554 or .B:558 or .B:515 or .B:517 or .B:518 or .B:519 or .B:520 or .B:522 or .B:548 or .B:558; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE38[A]
3.821
LEU43[A]
4.052
ARG64[A]
4.392
LEU184[A]
4.502
LEU186[A]
3.509
PRO187[A]
3.292
ALA189[A]
2.945
LYS190[A]
3.506
LYS191[A]
3.667
THR60[A]
3.941
ASN61[A]
3.173
LEU63[A]
4.866
ARG64[A]
3.356
VAL66[A]
3.537
GLY67[A]
3.142
LEU68[A]
4.013
Residue
Distance (Å)
GLU100[A]
3.546
ALA101[A]
3.619
GLY102[A]
3.769
GLU103[A]
4.383
MET548[B]
3.545
LEU554[B]
3.639
LEU558[B]
4.224
LEU515[B]
3.531
TYR517[B]
3.353
TRP518[B]
4.906
THR519[B]
3.508
THR520[B]
3.915
ASP522[B]
3.046
MET548[B]
3.552
LEU558[B]
3.922
Ligand Name: Bepridil, (R)- Ligand Info
Structure Description CRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH BEPRIDIL PDB:6F5U
Method X-ray diffraction Resolution 2.07 Å Mutation Yes [1]
PDB Sequence
.
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CQN or .CQN2 or .CQN3 or :3CQN;style chemicals stick;color identity;select .A:38 or .A:43 or .A:64 or .A:66 or .A:67 or .A:68 or .A:100 or .A:101 or .A:102 or .A:184 or .A:186 or .B:515 or .B:517 or .B:519 or .B:548 or .B:554 or .B:555 or .B:558; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE38[A]
4.601
LEU43[A]
4.001
ARG64[A]
3.129
VAL66[A]
3.473
GLY67[A]
4.586
LEU68[A]
4.432
GLU100[A]
4.775
ALA101[A]
3.486
GLY102[A]
3.859
Residue
Distance (Å)
LEU184[A]
3.993
LEU186[A]
3.892
LEU515[B]
3.492
TYR517[B]
3.525
THR519[B]
3.945
MET548[B]
3.387
LEU554[B]
4.199
ILE555[B]
4.319
LEU558[B]
3.303
Ligand Name: 10-{2-[(2r)-1-Methylpiperidin-2-Yl]ethyl}-2-(Methylsulfanyl)-10h-Phenothiazine Ligand Info
Structure Description Crystal structure of Ebolavirus glycoprotein in complex with thioridazine PDB:6G95
Method X-ray diffraction Resolution 2.31 Å Mutation Yes [2]
PDB Sequence
.
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .RTZ or .RTZ2 or .RTZ3 or :3RTZ;style chemicals stick;color identity;select .A:36 or .A:37 or .A:38 or .A:43 or .A:66 or .A:101 or .A:184 or .A:185 or .A:186 or .A:187 or .B:515 or .B:517 or .B:548 or .B:549 or .B:554 or .B:555 or .B:558; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY36[A]
3.133
VAL37[A]
3.504
ILE38[A]
3.648
LEU43[A]
3.442
VAL66[A]
4.001
ALA101[A]
4.121
LEU184[A]
3.675
ILE185[A]
2.959
LEU186[A]
3.679
Residue
Distance (Å)
PRO187[A]
4.118
LEU515[B]
3.959
TYR517[B]
4.015
MET548[B]
3.233
HIS549[B]
3.182
LEU554[B]
3.491
ILE555[B]
3.420
LEU558[B]
4.281
Ligand Name: (1R,3S,5S,7S)-N-[(1r,4R)-4-aminocyclohexyl]-3-[(methylsulfanyl)methyl]-5-phenyladamantane-1-carboxamide Ligand Info
Structure Description Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075146 PDB:7LYD
Method X-ray diffraction Resolution 2.35 Å Mutation Yes [6]
PDB Sequence
.
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .YOD or .YOD2 or .YOD3 or :3YOD;style chemicals stick;color identity;select .A:38 or .A:61 or .A:64 or .A:66 or .A:67 or .A:68 or .A:101 or .A:102 or .A:103 or .A:184 or .A:186 or .A:187 or .B:515 or .B:517 or .B:519 or .B:520 or .B:521 or .B:522 or .B:544 or .B:548 or .B:554 or .B:558; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE38[A]
4.190
ASN61[A]
4.949
ARG64[A]
3.111
VAL66[A]
3.396
GLY67[A]
3.620
LEU68[A]
4.066
ALA101[A]
3.750
GLY102[A]
3.647
GLU103[A]
4.468
LEU184[A]
4.227
LEU186[A]
3.497
Residue
Distance (Å)
PRO187[A]
4.453
LEU515[B]
3.567
TYR517[B]
3.576
THR519[B]
4.145
THR520[B]
3.724
GLN521[B]
4.324
ASP522[B]
4.810
ILE544[B]
4.482
MET548[B]
3.679
LEU554[B]
4.624
LEU558[B]
4.052
Ligand Name: (1R,3S,5R,7R)-N-[(1r,4R)-4-aminocyclohexyl]-3-(ethoxymethyl)-5-phenyladamantane-1-carboxamide Ligand Info
Structure Description Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0074953 PDB:7M2D
Method X-ray diffraction Resolution 2.70 Å Mutation Yes [7]
PDB Sequence
.
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .YPS or .YPS2 or .YPS3 or :3YPS;style chemicals stick;color identity;select .A:38 or .A:43 or .A:64 or .A:66 or .A:67 or .A:68 or .A:101 or .A:102 or .A:103 or .A:184 or .A:186 or .B:515 or .B:517 or .B:519 or .B:520 or .B:521 or .B:522 or .B:544 or .B:548 or .B:554 or .B:558; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE38[A]
4.125
LEU43[A]
4.941
ARG64[A]
3.040
VAL66[A]
3.374
GLY67[A]
3.661
LEU68[A]
4.053
ALA101[A]
3.827
GLY102[A]
3.556
GLU103[A]
4.404
LEU184[A]
4.067
LEU186[A]
3.544
Residue
Distance (Å)
LEU515[B]
3.457
TYR517[B]
3.577
THR519[B]
3.968
THR520[B]
3.605
GLN521[B]
4.206
ASP522[B]
4.738
ILE544[B]
4.473
MET548[B]
3.881
LEU554[B]
4.246
LEU558[B]
3.858
Ligand Name: (1s,3R,5S,7s)-N-[(1r,4r)-4-aminocyclohexyl]-3,5-diphenyladamantane-1-carboxamide Ligand Info
Structure Description Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075164 PDB:7LYY
Method X-ray diffraction Resolution 2.75 Å Mutation Yes [8]
PDB Sequence
.
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .YPM or .YPM2 or .YPM3 or :3YPM;style chemicals stick;color identity;select .A:38 or .A:64 or .A:66 or .A:67 or .A:68 or .A:101 or .A:102 or .A:103 or .A:184 or .A:186 or .A:187 or .B:515 or .B:517 or .B:519 or .B:520 or .B:521 or .B:522 or .B:544 or .B:548 or .B:554 or .B:558; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE38[A]
3.758
ARG64[A]
3.165
VAL66[A]
3.320
GLY67[A]
3.800
LEU68[A]
3.847
ALA101[A]
3.865
GLY102[A]
3.628
GLU103[A]
4.539
LEU184[A]
3.568
LEU186[A]
3.818
PRO187[A]
4.419
Residue
Distance (Å)
LEU515[B]
3.460
TYR517[B]
3.485
THR519[B]
4.299
THR520[B]
3.931
GLN521[B]
4.542
ASP522[B]
4.710
ILE544[B]
4.681
MET548[B]
3.513
LEU554[B]
3.606
LEU558[B]
4.149
Ligand Name: (1S,3R,5R,7S)-N-(trans-4-aminocyclohexyl)-3-methyl-5-phenyltricyclo[3.3.1.1~3,7~]decane-1-carboxamide Ligand Info
Structure Description Crystal Structure of Ebola zaire GP protein with bound ARN0074898 PDB:6NAE
Method X-ray diffraction Resolution 2.75 Å Mutation Yes [9]
PDB Sequence
.
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .KHG or .KHG2 or .KHG3 or :3KHG;style chemicals stick;color identity;select .A:64 or .A:66 or .A:67 or .A:68 or .A:101 or .A:102 or .A:103 or .A:184 or .A:186 or .B:515 or .B:517 or .B:518 or .B:519 or .B:544 or .B:548 or .B:558; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG64[A]
3.296
VAL66[A]
3.254
GLY67[A]
3.818
LEU68[A]
3.686
ALA101[A]
3.494
GLY102[A]
3.239
GLU103[A]
4.445
LEU184[A]
4.230
Residue
Distance (Å)
LEU186[A]
3.585
LEU515[B]
3.328
TYR517[B]
3.434
TRP518[B]
4.566
THR519[B]
4.574
ILE544[B]
4.828
MET548[B]
3.402
LEU558[B]
4.449
References  Top
REF 1 Target Identification and Mode of Action of Four Chemically Divergent Drugs against Ebolavirus Infection. J Med Chem. 2018 Feb 8;61(3):724-733.
REF 2 Structures of Ebola Virus Glycoprotein Complexes with Tricyclic Antidepressant and Antipsychotic Drugs. J Med Chem. 2018 Jun 14;61(11):4938-4945.
REF 3 Toremifene interacts with and destabilizes the Ebola virus glycoprotein. Nature. 2016 Jul 7;535(7610):169-172.
REF 4 Polyclonal and convergent antibody response to Ebola virus vaccine rVSV-ZEBOV. Nat Med. 2019 Oct;25(10):1589-1600.
REF 5 Structure-Based in Silico Screening Identifies a Potent Ebolavirus Inhibitor from a Traditional Chinese Medicine Library. J Med Chem. 2019 Mar 28;62(6):2928-2937.
REF 6 Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075146
REF 7 Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0074953
REF 8 Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075164
REF 9 Discovery of Adamantane Carboxamides as Ebola Virus Cell Entry and Glycoprotein Inhibitors. ACS Med Chem Lett. 2020 May 1;11(6):1160-1167.

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