Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T02702 Target Info
Target Name Bacterial Dihydrofolate reductase (Bact DHFR)
Synonyms Bact Dihydrofolate reductase
Target Type Clinical trial Target
Gene Name Bact DHFR
UniProt ID
DYR_ECOLI
Ligand General Information  Top
Ligand Name NADPH Ligand Info
Canonical SMILES C1C=CN(C=C1C(=O)N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)N4C=NC5=C(N=CN=C54)N)OP(=O)(O)O)O)O)O
InChI 1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKey ACFIXJIJDZMPPO-NNYOXOHSSA-N
PubChem Compound ID 5884
Drug Binding Sites of Target  Top
PDB ID: 5W3Q      L28F E.coli DHFR in complex with NADPH
Method X-ray diffraction Resolution 1.40 Å Mutation Yes [1]
PDB Sequence
MISLIAALAV
10
DRVIGMENAM
20
PWNLPADFAW
30
FKRNTLNKPV
40
IMGRHTWESI
50

GRPLPGRKNI
60
ILSSQPGTDD
70
RVTWVKSVDE
80
AIAACGDVPE
90
IMVIGGGRVY
100

EQFLPKAQKL
110
YLTHIDAEVE
120
GDTHFPDYEP
130
DDWESVFSEF
140
HDADAQNSHS
150

YCFEILERR
Residue
Distance (Å)
ILE5
4.220
ALA6
2.686
ALA7
1.966
LEU8
4.126
VAL13
4.901
ILE14
1.970
GLY15
2.378
MET16
3.499
GLU17
4.079
ASN18
2.094
ALA19
2.973
MET20
2.538
PRO21
4.868
TRP22
2.471
GLY43
2.625
ARG44
1.867
HIS45
2.195
THR46
1.940
TRP47
4.797
Residue
Distance (Å)
SER49
3.984
LEU62
2.159
SER63
1.829
SER64
1.968
GLN65
3.721
VAL75
4.520
LYS76
2.881
SER77
2.921
VAL78
2.788
ILE94
2.376
GLY95
2.507
GLY96
2.264
GLY97
2.483
ARG98
2.081
VAL99
2.543
TYR100
2.358
GLN102
1.840
ASP122
3.939
THR123
2.162
PDB ID: 3DAU      Crystal structure of the ternary MTX NADPH complex of Escherichia coli dihydrofolate reductase
Method X-ray diffraction Resolution 1.50 Å Mutation No [2]
PDB Sequence
MISLIAALAV
10
DRVIGMENAM
20
PWNLPADLAW
30
FKRNTLNKPV
40
IMGRHTWESI
50

GRPLPGRKNI
60
ILSSQPGTDD
70
RVTWVKSVDE
80
AIAACGDVPE
90
IMVIGGGRVY
100

EQFLPKAQKL
110
YLTHIDAEVE
120
GDTHFPDYEP
130
DDWESVFSEF
140
HDADAQNSHS
150

YCFEILERR
Residue
Distance (Å)
ILE5
4.669
ALA6
3.370
ALA7
2.774
ILE14
3.123
GLY15
3.278
MET16
3.564
GLU17
4.749
ASN18
3.666
ALA19
2.988
MET20
3.520
TRP22
3.478
GLY43
3.446
ARG44
2.650
HIS45
3.180
THR46
2.693
SER49
4.882
LEU62
3.164
Residue
Distance (Å)
SER63
2.564
SER64
2.697
GLN65
4.427
VAL75
4.832
LYS76
3.289
SER77
3.952
VAL78
3.989
ILE94
3.257
GLY95
3.722
GLY96
2.946
GLY97
3.094
ARG98
2.685
VAL99
3.410
TYR100
3.239
GLN102
2.848
ASP122
4.418
THR123
3.975
PDB ID: 4PDJ      Neutron crystal Structure of E.coli Dihydrofolate Reductase complexed with folate and NADP+
Method X-ray diffraction Resolution 1.60 Å Mutation No [3]
PDB Sequence
MISLIAALAV
10
DRVIGMENAM
20
PWNLPADLAW
30
FKRNTLNKPV
40
IMGRHTWESI
50

GRPLPGRKNI
60
ILSSQPGTDD
70
RVTWVKSVDE
80
AIAACGDVPE
90
IMVIGGGRVY
100

EQFLPKAQKL
110
YLTHIDAEVE
120
GDTHFPDYEP
130
DDWESVFSEF
140
HDADAQNSHS
150

YCFEILERR
Residue
Distance (Å)
ILE5
4.337
ALA6
2.573
ALA7
1.806
LEU8
4.209
VAL13
4.985
ILE14
2.103
GLY15
2.545
MET16
3.649
GLU17
4.683
ASN18
2.335
ALA19
3.038
MET20
2.713
TRP22
2.414
GLY43
2.392
ARG44
2.044
HIS45
2.340
THR46
1.738
TRP47
4.883
SER49
3.000
ILE50
4.972
Residue
Distance (Å)
LEU62
2.282
SER63
1.939
SER64
1.754
GLN65
3.499
VAL75
4.740
LYS76
3.011
SER77
2.693
VAL78
2.343
ILE94
2.227
GLY95
2.583
GLY96
1.849
GLY97
2.365
ARG98
1.951
VAL99
2.492
TYR100
2.622
GLN102
2.260
ILE115
4.878
ASP122
4.034
THR123
2.668
PDB ID: 3QYL      Sensitivity of receptor internal motions to ligand binding affinity and kinetic off-rate
Method X-ray diffraction Resolution 1.79 Å Mutation No [4]
PDB Sequence
MISLIAALAV
10
DRVIGMENAM
20
PWNLPADLAW
30
FKRNTLDKPV
40
IMGRHTWESI
50

GRPLPGRKNI
60
ILSSQPGTDD
70
RVTWVKSVDE
80
AIAACGDVPE
90
IMVIGGGRVY
100

EQFLPKAQKL
110
YLTHIDAEVE
120
GDTHFPDYEP
130
DDWESVFSEF
140
HDADAQNSHS
150

YCFEILERR
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NDP or .NDP2 or .NDP3 or :3NDP;style chemicals stick;color identity;select .A:5 or .A:6 or .A:7 or .A:14 or .A:15 or .A:16 or .A:17 or .A:18 or .A:19 or .A:20 or .A:22 or .A:43 or .A:44 or .A:45 or .A:46 or .A:49 or .A:62 or .A:63 or .A:64 or .A:65 or .A:75 or .A:76 or .A:77 or .A:78 or .A:94 or .A:95 or .A:96 or .A:97 or .A:98 or .A:99 or .A:100 or .A:102 or .A:122 or .A:123; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE5
4.740
ALA6
3.444
ALA7
2.765
ILE14
2.985
GLY15
3.579
MET16
3.853
GLU17
4.920
ASN18
3.441
ALA19
3.288
MET20
3.560
TRP22
3.573
GLY43
3.320
ARG44
2.814
HIS45
3.402
THR46
2.601
SER49
3.521
LEU62
3.198
Residue
Distance (Å)
SER63
2.668
SER64
2.638
GLN65
4.434
VAL75
4.653
LYS76
3.116
SER77
3.864
VAL78
3.844
ILE94
3.072
GLY95
3.771
GLY96
2.987
GLY97
3.343
ARG98
2.952
VAL99
3.219
TYR100
3.495
GLN102
2.850
ASP122
4.470
THR123
3.674
PDB ID: 3KFY      Dynamic switching and partial occupancies of a small molecule inhibitor complex of DHFR
Method X-ray diffraction Resolution 2.08 Å Mutation Yes [5]
PDB Sequence
MISLIAALAV
10
DRVIGMENAM
20
PWNLPADLAW
30
FKRNTLDKPV
40
IMGRHTWESI
50

GRPLPGRKNI
60
ILSSQPGTDD
70
RVTWVKSVDE
80
AIAACGDVPE
90
IMVIGGGRVY
100

EQFLPKAQKL
110
YLTHIDAEVE
120
GDTHFPDYEP
130
DDWESVFSEF
140
HDADAQNSHS
150

YCFEILERR
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NDP or .NDP2 or .NDP3 or :3NDP;style chemicals stick;color identity;select .A:18 or .A:43 or .A:44 or .A:45 or .A:46 or .A:62 or .A:63 or .A:64 or .A:65 or .A:75 or .A:76 or .A:77 or .A:78 or .A:95 or .A:96 or .A:97 or .A:98 or .A:99 or .A:102 or .A:123; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN18
4.344
GLY43
3.402
ARG44
2.757
HIS45
3.370
THR46
2.741
LEU62
2.833
SER63
2.572
SER64
2.767
GLN65
4.261
VAL75
4.898
Residue
Distance (Å)
LYS76
3.255
SER77
4.038
VAL78
3.992
GLY95
3.966
GLY96
3.008
GLY97
3.179
ARG98
2.972
VAL99
3.474
GLN102
2.706
THR123
3.993
PDB ID: 3QYO      Sensitivity of receptor internal motions to ligand binding affinity and kinetic off-rate
Method X-ray diffraction Resolution 2.09 Å Mutation No [4]
PDB Sequence
MISLIAALAV
10
DRVIGMENAM
20
PWNLPADLAW
30
FKRNTLDKPV
40
IMGRHTWESI
50

GRPLPGRKNI
60
ILSSQPGTDD
70
RVTWVKSVDE
80
AIAACGDVPE
90
IMVIGGGRVY
100

EQFLPKAQKL
110
YLTHIDAEVE
120
GDTHFPDYEP
130
DDWESVFSEF
140
HDADAQNSHS
150

YCFEILERR
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NDP or .NDP2 or .NDP3 or :3NDP;style chemicals stick;color identity;select .A:5 or .A:6 or .A:7 or .A:14 or .A:15 or .A:16 or .A:17 or .A:18 or .A:19 or .A:20 or .A:22 or .A:43 or .A:44 or .A:45 or .A:46 or .A:49 or .A:62 or .A:63 or .A:64 or .A:65 or .A:75 or .A:76 or .A:77 or .A:78 or .A:94 or .A:95 or .A:96 or .A:97 or .A:98 or .A:99 or .A:100 or .A:102 or .A:122 or .A:123; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE5
4.759
ALA6
3.414
ALA7
2.790
ILE14
2.958
GLY15
3.675
MET16
3.946
GLU17
4.750
ASN18
3.389
ALA19
3.430
MET20
3.626
TRP22
3.559
GLY43
3.310
ARG44
2.701
HIS45
3.405
THR46
2.601
SER49
3.914
LEU62
3.180
Residue
Distance (Å)
SER63
2.641
SER64
2.684
GLN65
4.422
VAL75
4.749
LYS76
3.223
SER77
3.849
VAL78
3.925
ILE94
3.099
GLY95
3.950
GLY96
3.004
GLY97
3.238
ARG98
2.832
VAL99
3.242
TYR100
3.546
GLN102
2.798
ASP122
4.498
THR123
3.549
PDB ID: 3R33      Evidence for dynamic motion in proteins as a mechanism for ligand dissociation
Method X-ray diffraction Resolution 2.09 Å Mutation No [4]
PDB Sequence
MISLIAALAV
10
DRVIGMENAM
20
PWNLPADLAW
30
FKRNTLDKPV
40
IMGRHTWESI
50

GRPLPGRKNI
60
ILSSQPGTDD
70
RVTWVKSVDE
80
AIAACGDVPE
90
IMVIGGGRVY
100

EQFLPKAQKL
110
YLTHIDAEVE
120
GDTHFPDYEP
130
DDWESVFSEF
140
HDADAQNSHS
150

YCFEILERR
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NDP or .NDP2 or .NDP3 or :3NDP;style chemicals stick;color identity;select .A:5 or .A:6 or .A:7 or .A:14 or .A:15 or .A:16 or .A:17 or .A:18 or .A:19 or .A:20 or .A:22 or .A:43 or .A:44 or .A:45 or .A:46 or .A:62 or .A:63 or .A:64 or .A:65 or .A:75 or .A:76 or .A:77 or .A:78 or .A:94 or .A:95 or .A:96 or .A:97 or .A:98 or .A:99 or .A:100 or .A:102 or .A:122 or .A:123; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE5
4.793
ALA6
3.411
ALA7
2.824
ILE14
2.908
GLY15
3.554
MET16
3.881
GLU17
4.826
ASN18
3.438
ALA19
3.316
MET20
3.613
TRP22
3.650
GLY43
3.416
ARG44
2.763
HIS45
3.432
THR46
2.733
LEU62
3.189
SER63
2.702
Residue
Distance (Å)
SER64
2.688
GLN65
4.378
VAL75
4.709
LYS76
3.261
SER77
3.873
VAL78
4.001
ILE94
3.154
GLY95
3.846
GLY96
2.935
GLY97
3.172
ARG98
2.867
VAL99
3.407
TYR100
3.433
GLN102
2.701
ASP122
4.543
THR123
3.579
PDB ID: 2ANQ      Crystal Structure of E.coli DHFR in complex with NADPH and the inhibitor compound 10a.
Method X-ray diffraction Resolution 2.13 Å Mutation Yes [6]
PDB Sequence
MISLIAALAV
10
DRVIGMENAM
20
PWNLPADLAW
30
FKRNTLDKPV
40
IMGRHTWESI
50

GRPLPGRKNI
60
ILSSQPGTDD
70
RVTWVKSVDE
80
AIAACGDVPE
90
IMVIGGGRVY
100

EQFLPKAQKL
110
YLTHIDAEVE
120
GDTHFPDYEP
130
DDWESVFSEF
140
HDADAQNSHS
150

YCFEILERR
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NDP or .NDP2 or .NDP3 or :3NDP;style chemicals stick;color identity;select .A:5 or .A:6 or .A:7 or .A:14 or .A:15 or .A:16 or .A:17 or .A:18 or .A:19 or .A:20 or .A:22 or .A:43 or .A:44 or .A:45 or .A:46 or .A:49 or .A:62 or .A:63 or .A:64 or .A:65 or .A:75 or .A:76 or .A:77 or .A:78 or .A:94 or .A:95 or .A:96 or .A:97 or .A:98 or .A:99 or .A:100 or .A:102 or .A:122 or .A:123; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE5
4.475
ALA6
3.274
ALA7
2.731
ILE14
2.753
GLY15
3.723
MET16
3.951
GLU17
4.591
ASN18
3.122
ALA19
3.169
MET20
3.462
TRP22
3.659
GLY43
3.348
ARG44
2.958
HIS45
3.417
THR46
2.697
SER49
4.111
LEU62
2.593
Residue
Distance (Å)
SER63
2.358
SER64
2.635
GLN65
4.046
VAL75
4.975
LYS76
3.283
SER77
3.879
VAL78
3.912
ILE94
2.731
GLY95
3.399
GLY96
3.035
GLY97
3.337
ARG98
2.997
VAL99
3.274
TYR100
2.860
GLN102
2.401
ASP122
4.378
THR123
3.847
PDB ID: 2ANO      Crystal structure of E.coli dihydrofolate reductase in complex with NADPH and the inhibitor MS-SH08-17
Method X-ray diffraction Resolution 2.68 Å Mutation Yes [6]
PDB Sequence
MISLIAALAV
10
DRVIGMENAM
20
PWNLPADLAW
30
FKRNTLDKPV
40
IMGRHTWESI
50

GRPLPGRKNI
60
ILSSQPGTDD
70
RVTWVKSVDE
80
AIAACGDVPE
90
IMVIGGGRVY
100

EQFLPKAQKL
110
YLTHIDAEVE
120
GDTHFPDYEP
130
DDWESVFSEF
140
HDADAQNSHS
150

YCFEILERR
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NDP or .NDP2 or .NDP3 or :3NDP;style chemicals stick;color identity;select .A:5 or .A:6 or .A:7 or .A:14 or .A:15 or .A:16 or .A:17 or .A:18 or .A:19 or .A:20 or .A:22 or .A:42 or .A:43 or .A:44 or .A:45 or .A:46 or .A:49 or .A:62 or .A:63 or .A:64 or .A:65 or .A:76 or .A:77 or .A:78 or .A:94 or .A:95 or .A:96 or .A:97 or .A:98 or .A:99 or .A:100 or .A:102 or .A:122 or .A:123; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE5
4.466
ALA6
3.165
ALA7
2.752
ILE14
2.809
GLY15
3.207
MET16
3.215
GLU17
4.725
ASN18
3.307
ALA19
3.135
MET20
3.453
TRP22
3.696
MET42
4.974
GLY43
3.346
ARG44
3.108
HIS45
3.470
THR46
2.639
SER49
4.650
Residue
Distance (Å)
LEU62
2.941
SER63
2.528
SER64
2.853
GLN65
4.156
LYS76
3.413
SER77
4.029
VAL78
4.108
ILE94
3.060
GLY95
3.993
GLY96
3.085
GLY97
2.774
ARG98
2.927
VAL99
3.345
TYR100
3.057
GLN102
2.460
ASP122
4.884
THR123
3.883
PDB ID: 4GH8      Crystal structure of a 'humanized' E. coli dihydrofolate reductase
Method X-ray diffraction Resolution 1.85 Å Mutation No [7]
PDB Sequence
MISLIAALAV
10
DRVIGMENAM
20
PWPPLPADLA
30
WFKRNTLNKP
40
VIMGRHTWES
50

IPEKNRPLPG
60
RKNIILSSQP
70
GTDDRVTWVK
80
SVDEAIAACG
90
DVPEIMVIGG
100

GRVYEQFLPK
110
AQKLYLTHID
120
AEVEGDTHFP
130
DYEPDDWESV
140
FSEFHDADAQ
150

NSHSYCFEIL
160
ER
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NDP or .NDP2 or .NDP3 or :3NDP;style chemicals stick;color identity;select .B:5 or .B:6 or .B:7 or .B:14 or .B:15 or .B:16 or .B:17 or .B:18 or .B:19 or .B:20 or .B:22 or .B:44 or .B:45 or .B:46 or .B:47 or .B:50 or .B:66 or .B:67 or .B:68 or .B:69 or .B:79 or .B:80 or .B:81 or .B:82 or .B:98 or .B:99 or .B:100 or .B:101 or .B:102 or .B:103 or .B:104 or .B:106 or .B:126 or .B:127; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE5
4.777
ALA6
3.481
ALA7
2.849
ILE14
3.165
GLY15
3.413
MET16
3.734
GLU17
4.716
ASN18
3.339
ALA19
3.318
MET20
3.778
TRP22
3.907
GLY44
3.460
ARG45
2.602
HIS46
3.418
THR47
2.844
SER50
4.234
LEU66
3.021
Residue
Distance (Å)
SER67
2.625
SER68
2.710
GLN69
4.265
VAL79
4.944
LYS80
3.247
SER81
3.831
VAL82
3.880
ILE98
3.200
GLY99
3.822
GLY100
3.006
GLY101
3.160
ARG102
2.856
VAL103
3.290
TYR104
3.327
GLN106
2.926
ASP126
4.711
THR127
3.995
PDB ID: 6XG5      X-ray structure of Escherichia coli dihydrofolate reductase in complex with trimethoprim
Method X-ray diffraction Resolution 1.90 Å Mutation No [8]
PDB Sequence
MISLIAALAV
10
DRVIGMENAM
20
PWNLPADLAW
30
FKRNTLNKPV
40
IMGRHTWESI
50

GRPLPGRKNI
60
ILSSQPGTDD
70
RVTWVKSVDE
80
AIAACGDVPE
90
IMVIGGGRVY
100

EQFLPKAQKL
110
YLTHIDAEVE
120
GDTHFPDYEP
130
DDWESVFSEF
140
HDADAQNSHS
150

YCFEILERR
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NDP or .NDP2 or .NDP3 or :3NDP;style chemicals stick;color identity;select .A:5 or .A:6 or .A:7 or .A:8 or .A:14 or .A:15 or .A:16 or .A:17 or .A:18 or .A:19 or .A:20 or .A:22 or .A:43 or .A:44 or .A:45 or .A:46 or .A:49 or .A:62 or .A:63 or .A:64 or .A:65 or .A:75 or .A:76 or .A:77 or .A:78 or .A:94 or .A:95 or .A:96 or .A:97 or .A:98 or .A:99 or .A:100 or .A:102 or .A:122 or .A:123; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE5
4.707
ALA6
3.269
ALA7
2.712
LEU8
4.935
ILE14
2.974
GLY15
3.435
MET16
3.727
GLU17
4.838
ASN18
3.447
ALA19
3.125
MET20
3.613
TRP22
3.752
GLY43
3.427
ARG44
3.001
HIS45
3.274
THR46
2.788
SER49
4.248
LEU62
3.033
Residue
Distance (Å)
SER63
2.697
SER64
2.734
GLN65
3.268
VAL75
4.983
LYS76
3.297
SER77
3.938
VAL78
4.042
ILE94
3.306
GLY95
3.909
GLY96
3.145
GLY97
3.047
ARG98
2.690
VAL99
3.377
TYR100
3.426
GLN102
2.846
ASP122
4.412
THR123
3.950
PDB ID: 6XG4      X-ray structure of Escherichia coli dihydrofolate reductase L28R mutant in complex with trimethoprim
Method X-ray diffraction Resolution 2.10 Å Mutation Yes [8]
PDB Sequence
MISLIAALAV
10
DRVIGMENAM
20
PWNLPADRAW
30
FKRNTLNKPV
40
IMGRHTWESI
50

GRPLPGRKNI
60
ILSSQPGTDD
70
RVTWVKSVDE
80
AIAACGDVPE
90
IMVIGGGRVY
100

EQFLPKAQKL
110
YLTHIDAEVE
120
GDTHFPDYEP
130
DDWESVFSEF
140
HDADAQNSHS
150

YCFEILERR
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NDP or .NDP2 or .NDP3 or :3NDP;style chemicals stick;color identity;select .A:5 or .A:6 or .A:7 or .A:8 or .A:14 or .A:15 or .A:16 or .A:17 or .A:18 or .A:19 or .A:20 or .A:22 or .A:43 or .A:44 or .A:45 or .A:46 or .A:49 or .A:62 or .A:63 or .A:64 or .A:65 or .A:75 or .A:76 or .A:77 or .A:78 or .A:94 or .A:95 or .A:96 or .A:97 or .A:98 or .A:99 or .A:100 or .A:102 or .A:122 or .A:123; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE5
4.696
ALA6
3.274
ALA7
2.699
LEU8
4.987
ILE14
3.002
GLY15
3.375
MET16
3.848
GLU17
4.673
ASN18
3.322
ALA19
3.022
MET20
3.481
TRP22
3.831
GLY43
3.381
ARG44
3.058
HIS45
3.214
THR46
2.702
SER49
4.043
LEU62
3.199
Residue
Distance (Å)
SER63
2.487
SER64
2.768
GLN65
3.799
VAL75
4.926
LYS76
3.136
SER77
3.828
VAL78
3.593
ILE94
3.219
GLY95
3.761
GLY96
2.987
GLY97
2.929
ARG98
2.825
VAL99
3.308
TYR100
3.377
GLN102
2.946
ASP122
4.340
THR123
3.864
PDB ID: 6RUM      Crystal structure of GFP-LAMA-G97 - a GFP enhancer nanobody with cpDHFR insertion and TMP and NADPH
Method X-ray diffraction Resolution 1.60 Å Mutation No [9]
PDB Sequence
QVQLVESGGA
10
LVQPGGSLRL
20
SCAASGFPVN
30
RYSMRWYRQA
40
PGKEREWVAG
50

MSSAGDRSSY
59
EDSVKGRFTI
69
SRDDARNTVY
79
LQMNSLKPED
86
TAVYYCNVNV
96

GLPADLAWFK
106
RNTLNKPVIM
116
GRHTWESIGR
126
PLPGRKNIIL
136
SSQPGTDDRV
146

TWVKSVDEAI
156
AACGDVPEIM
166
VIGGGRVYEQ
176
FLPKAQKLYL
186
THIDAEVEGD
196

THFPDYEPDD
206
WESVFSEFHD
216
ADAQNSHSYC
226
FEILERRGGG
238
MISLIAALAV
248

DRVIGMENAM
258
PWNFEYWGQG
268
TQVTVS
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NDP or .NDP2 or .NDP3 or :3NDP;style chemicals stick;color identity;select .A:117 or .A:118 or .A:119 or .A:120 or .A:123 or .A:136 or .A:137 or .A:138 or .A:139 or .A:149 or .A:150 or .A:151 or .A:152 or .A:168 or .A:169 or .A:170 or .A:171 or .A:172 or .A:173 or .A:174 or .A:176 or .A:196 or .A:197 or .A:243 or .A:244 or .A:245 or .A:252 or .A:253 or .A:254 or .A:255 or .A:256 or .A:257 or .A:258 or .A:260; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY117
3.316
ARG118
2.570
HIS119
2.990
THR120
2.783
SER123
4.220
LEU136
3.267
SER137
2.629
SER138
2.690
GLN139
4.467
VAL149
4.689
LYS150
3.263
SER151
3.792
VAL152
4.004
ILE168
3.269
GLY169
3.811
GLY170
3.072
GLY171
3.058
Residue
Distance (Å)
ARG172
2.759
VAL173
3.188
TYR174
3.513
GLN176
2.828
ASP196
4.516
THR197
3.819
ILE243
4.752
ALA244
3.478
ALA245
2.844
ILE252
3.107
GLY253
3.388
MET254
3.744
GLU255
4.836
ASN256
3.375
ALA257
3.298
MET258
3.624
TRP260
3.668
PDB ID: 6RUL      Crystal structure of GFP-LAMA-F98 - a GFP enhancer nanobody with cpDHFR insertion and TMP and NADPH
Method X-ray diffraction Resolution 2.20 Å Mutation No [9]
PDB Sequence
QVQLVESGGA
10
LVQPGGSLRL
20
SCAASGFPVN
30
RYSMRWYRQA
40
PGKEREWVAG
50

MSSAGDRSSY
59
EDSVKGRFTI
69
SRDDARNTVY
79
LQMNSLKPED
86
TAVYYCNVNV
96

GFLPADLAWF
106
KRNTLNKPVI
116
MGRHTWESIG
126
RPLPGRKNII
136
LSSQPGTDDR
146

VTWVKSVDEA
156
IAACGDVPEI
166
MVIGGGRVYE
176
QFLPKAQKLY
186
LTHIDAEVEG
196

DTHFPDYEPD
206
DWESVFSEFH
216
DADAQNSHSY
226
CFEILERRGG
236
GMISLIAALA
248

VDRVIGMENA
258
MPWNEYWGQG
268
TQVTVS
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NDP or .NDP2 or .NDP3 or :3NDP;style chemicals stick;color identity;select .A:118 or .A:119 or .A:120 or .A:121 or .A:124 or .A:137 or .A:138 or .A:139 or .A:140 or .A:150 or .A:151 or .A:152 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:177 or .A:197 or .A:198 or .A:244 or .A:245 or .A:246 or .A:253 or .A:254 or .A:255 or .A:256 or .A:257 or .A:258 or .A:259 or .A:261; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY118
3.166
ARG119
2.499
HIS120
3.007
THR121
2.803
SER124
3.507
LEU137
3.002
SER138
2.382
SER139
2.442
GLN140
3.200
VAL150
4.694
LYS151
3.184
SER152
3.990
VAL153
3.898
ILE169
3.317
GLY170
3.839
GLY171
2.945
GLY172
2.886
Residue
Distance (Å)
ARG173
2.601
VAL174
3.053
TYR175
3.462
GLN177
2.868
ASP197
4.551
THR198
3.506
ILE244
4.759
ALA245
3.409
ALA246
2.723
ILE253
2.962
GLY254
3.647
MET255
3.793
GLU256
4.471
ASN257
3.276
ALA258
3.491
MET259
4.091
TRP261
3.574
References  Top
REF 1 Defining the Structural Basis for Allosteric Product Release from E. coli Dihydrofolate Reductase Using NMR Relaxation Dispersion. J Am Chem Soc. 2017 Aug 16;139(32):11233-11240.
REF 2 X-ray structure of the ternary MTX.NADPH complex of the anthrax dihydrofolate reductase: a pharmacophore for dual-site inhibitor design. J Struct Biol. 2009 May;166(2):162-71.
REF 3 Toward resolving the catalytic mechanism of dihydrofolate reductase using neutron and ultrahigh-resolution X-ray crystallography. Proc Natl Acad Sci U S A. 2014 Dec 23;111(51):18225-30.
REF 4 Evidence for dynamics in proteins as a mechanism for ligand dissociation. Nat Chem Biol. 2012 Jan 15;8(3):246-52.
REF 5 Dynamic switching and partial occupancies of a small molecule inhibitor complex of DHFR
REF 6 A 2.13 A structure of E. coli dihydrofolate reductase bound to a novel competitive inhibitor reveals a new binding surface involving the M20 loop region. J Med Chem. 2006 Nov 30;49(24):6977-86.
REF 7 Functional significance of evolving protein sequence in dihydrofolate reductase from bacteria to humans. Proc Natl Acad Sci U S A. 2013 Jun 18;110(25):10159-64.
REF 8 A trimethoprim derivative impedes antibiotic resistance evolution. Nat Commun. 2021 May 19;12(1):2949.
REF 9 Chemogenetic Control of Nanobodies. Nat Methods. 2020 Mar;17(3):279-282.

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