Receptor
PDB id Resolution Class Description Source Keywords
4DP3 2.4 Å EC: 1.5.1.3 QUADRUPLE MUTANT (N51I+C59R+S108N+I164L) PLASMODIUM FALCIPAR DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE (PFDHFR-TS) COW ITH P218 AND NADPH PLASMODIUM FALCIPARUM ROSSMANN FOLD REDUCTASE OXIDOREDUCTASE TRANSFERASE-INHIBICOMPLEX
Ref.: MALARIAL DIHYDROFOLATE REDUCTASE AS A PARADIGM FOR DEVELOPMENT AGAINST A RESISTANCE-COMPROMISED TARGET PROC.NATL.ACAD.SCI.USA V. 109 16823 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MMV A:701;
B:701;
Valid;
Valid;
none;
none;
Ki = 0.54 nM
360.408 C18 H24 N4 O4 CCc1c...
NDP A:702;
B:702;
Valid;
Valid;
none;
none;
submit data
745.421 C21 H30 N7 O17 P3 c1nc(...
PO4 A:703;
B:703;
Invalid;
Invalid;
none;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4DP3 2.4 Å EC: 1.5.1.3 QUADRUPLE MUTANT (N51I+C59R+S108N+I164L) PLASMODIUM FALCIPAR DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE (PFDHFR-TS) COW ITH P218 AND NADPH PLASMODIUM FALCIPARUM ROSSMANN FOLD REDUCTASE OXIDOREDUCTASE TRANSFERASE-INHIBICOMPLEX
Ref.: MALARIAL DIHYDROFOLATE REDUCTASE AS A PARADIGM FOR DEVELOPMENT AGAINST A RESISTANCE-COMPROMISED TARGET PROC.NATL.ACAD.SCI.USA V. 109 16823 2012
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 3QG2 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 4DP3 Ki = 0.54 nM MMV C18 H24 N4 O4 CCc1c(c(nc....
3 3QGT - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
4 4DPD - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
5 3UM5 Ki = 0.6 nM CP6 C12 H13 Cl N4 CCc1c(c(nc....
6 4DPH Ki = 5.59 nM P65 C14 H15 Cl3 N4 O2 Cc1c(c(nc(....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 3QG2 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 4DP3 Ki = 0.54 nM MMV C18 H24 N4 O4 CCc1c(c(nc....
3 3QGT - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
4 4DPD - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
5 3UM5 Ki = 0.6 nM CP6 C12 H13 Cl N4 CCc1c(c(nc....
6 4DPH Ki = 5.59 nM P65 C14 H15 Cl3 N4 O2 Cc1c(c(nc(....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 3QG2 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 4DP3 Ki = 0.54 nM MMV C18 H24 N4 O4 CCc1c(c(nc....
3 3QGT - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
4 4DPD - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
5 3UM5 Ki = 0.6 nM CP6 C12 H13 Cl N4 CCc1c(c(nc....
6 4DPH Ki = 5.59 nM P65 C14 H15 Cl3 N4 O2 Cc1c(c(nc(....
7 4EIL - UMP C9 H13 N2 O8 P C1[C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MMV; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 MMV 1 1
Ligand no: 2; Ligand: NDP; Similar ligands found: 159
No: Ligand ECFP6 Tc MDL keys Tc
1 NDP 1 1
2 0WD 0.827273 1
3 NAI 0.803738 0.986842
4 NMN AMP PO4 0.794643 0.948052
5 NPW 0.692308 0.962025
6 NZQ 0.686441 0.987013
7 DG1 0.68 1
8 1DG 0.68 1
9 A2R 0.650943 0.909091
10 A22 0.64486 0.934211
11 TXP 0.644628 0.924051
12 ATR 0.640777 0.894737
13 NA7 0.636364 0.886076
14 XNP 0.620968 0.949367
15 AP0 0.598361 0.948718
16 A2P 0.598039 0.881579
17 NJP 0.574803 0.923077
18 25L 0.550847 0.934211
19 ODP 0.550388 0.936709
20 NAX 0.544 0.949367
21 25A 0.53913 0.921053
22 2AM 0.529412 0.87013
23 6V0 0.519685 0.974026
24 NAP 0.514493 0.922078
25 EAD 0.507143 0.949367
26 A2D 0.504673 0.921053
27 TXE 0.503876 0.935897
28 NA0 0.496454 0.910256
29 TXD 0.496124 0.911392
30 SAP 0.495575 0.875
31 AGS 0.495575 0.875
32 P1H 0.493056 0.925926
33 CO7 0.489796 0.791209
34 TAP 0.489362 0.864198
35 PAP 0.482456 0.907895
36 BA3 0.481818 0.921053
37 NAJ PZO 0.478261 0.924051
38 ATP 0.477876 0.921053
39 B4P 0.477477 0.921053
40 ADP 0.477477 0.921053
41 AP5 0.477477 0.921053
42 OAD 0.47541 0.897436
43 5FA 0.473684 0.921053
44 AR6 0.473684 0.896104
45 APR 0.473684 0.896104
46 AQP 0.473684 0.921053
47 AN2 0.473214 0.909091
48 3OD 0.467742 0.897436
49 50T 0.464912 0.884615
50 PO4 PO4 A A A A PO4 0.463415 0.857143
51 V3L 0.461538 0.896104
52 2A5 0.46087 0.85
53 A1R 0.459016 0.841463
54 ADQ 0.459016 0.897436
55 4AD 0.459016 0.875
56 OVE 0.458716 0.8375
57 OMR 0.458647 0.813953
58 PPS 0.457627 0.811765
59 AD9 0.456897 0.897436
60 CA0 0.45614 0.897436
61 M33 0.45614 0.884615
62 ADJ 0.455882 0.879518
63 A3P 0.455357 0.894737
64 ACP 0.452174 0.897436
65 ENP 0.451613 0.85
66 UP5 0.451128 0.948052
67 SRP 0.45 0.8625
68 ANP 0.449153 0.897436
69 ACQ 0.449153 0.897436
70 PRX 0.448276 0.82716
71 5AL 0.445378 0.884615
72 7D4 0.443478 0.8375
73 ADX 0.443478 0.811765
74 AMP 0.436364 0.894737
75 A 0.436364 0.894737
76 4TC 0.433824 0.924051
77 7D3 0.433628 0.8375
78 ETB 0.433566 0.797753
79 DCA 0.433566 0.788889
80 1ZZ 0.433071 0.802326
81 BIS 0.433071 0.864198
82 00A 0.432 0.864198
83 ATF 0.429752 0.886076
84 0T1 0.427586 0.788889
85 5SV 0.427419 0.788235
86 8QN 0.427419 0.884615
87 3AM 0.427273 0.857143
88 N01 0.426573 0.884615
89 PR8 0.425197 0.811765
90 WAQ 0.425197 0.841463
91 LAD 0.425197 0.821429
92 DTP 0.425 0.8375
93 AMO 0.424 0.886076
94 PAJ 0.424 0.843373
95 APC 0.423729 0.886076
96 UPA 0.423358 0.935897
97 48N 0.422222 0.853659
98 FYA 0.421875 0.860759
99 PTJ 0.421875 0.853659
100 CNA 0.421429 0.910256
101 PUA 0.42069 0.9125
102 NXX 0.419118 0.910256
103 DND 0.419118 0.910256
104 AV2 0.418033 0.848101
105 COA 0.417808 0.788889
106 3UK 0.417323 0.897436
107 OOB 0.416 0.909091
108 IVC 0.415584 0.78022
109 DAT 0.415254 0.8375
110 NDO 0.414966 0.897436
111 139 0.414286 0.901235
112 3AT 0.413223 0.896104
113 TAT 0.413223 0.886076
114 YLB 0.413043 0.784091
115 62F 0.4125 0.823529
116 ABM 0.412281 0.848101
117 YAP 0.412214 0.875
118 YLP 0.411765 0.784091
119 ME8 0.410853 0.802326
120 NB8 0.410853 0.853659
121 SON 0.410256 0.886076
122 DLL 0.409449 0.909091
123 AHX 0.409449 0.853659
124 COS 0.409396 0.771739
125 AMX 0.409396 0.797753
126 CAO 0.409396 0.763441
127 30N 0.409396 0.72449
128 7D5 0.409091 0.8125
129 4UW 0.408759 0.9125
130 APX 0.407692 0.841463
131 SRA 0.40708 0.85
132 CMX 0.406667 0.788889
133 SCO 0.406667 0.788889
134 TYM 0.405797 0.886076
135 COD 0.405594 0.777778
136 OXK 0.405229 0.771739
137 CA6 0.405229 0.70297
138 A12 0.405172 0.886076
139 AP2 0.405172 0.886076
140 9SN 0.40458 0.853659
141 LAQ 0.404412 0.802326
142 T5A 0.404255 0.914634
143 FAM 0.403974 0.771739
144 ACO 0.403974 0.763441
145 FCX 0.403974 0.763441
146 AMP MG 0.403509 0.825
147 VO4 ADP 0.403226 0.860759
148 ADP VO4 0.403226 0.860759
149 YLC 0.402878 0.823529
150 1VU 0.402597 0.763441
151 FA5 0.401515 0.886076
152 HAX 0.401316 0.771739
153 APU 0.4 0.923077
154 TXA 0.4 0.886076
155 A U 0.4 0.898734
156 4UU 0.4 0.948052
157 AFH 0.4 0.843373
158 CAJ 0.4 0.771739
159 AR6 AR6 0.4 0.871795
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4DP3; Ligand: NDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4dp3.bio1) has 38 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4DP3; Ligand: NDP; Similar sites found: 33
This union binding pocket(no: 2) in the query (biounit: 4dp3.bio1) has 45 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1YQT ADP 0.0175 0.44044 1.48699
2 2ACV UDP 0.01439 0.42579 1.72786
3 3CV2 COA 0.0142 0.4519 1.8797
4 1WD4 AHR 0.04974 0.40814 2.6971
5 2YVK MRU 0.02711 0.40557 3.125
6 4WOV 3SM 0.03683 0.40824 3.15457
7 2VZ6 FEF 0.02627 0.41951 3.19489
8 2VGD XYP XYP XYP FX3 0.0452 0.40044 3.21101
9 3B5J 12D 0.03205 0.42261 3.29218
10 1NLM UD1 0.03489 0.40021 3.2967
11 1U5R ATP 0.02429 0.40791 3.44828
12 5GOE GDP 0.0407 0.40279 3.5545
13 5MOB A8S 0.03938 0.41012 3.87931
14 1TZJ A3B 0.02295 0.43268 4.14201
15 4RW3 SHV 0.04358 0.4306 4.63576
16 3B6C SDN 0.01407 0.44255 4.70085
17 4WZ6 ATP 0.03755 0.42084 4.82759
18 2H8H H8H 0.03337 0.40115 4.85981
19 4BGB ADP 0.02495 0.42071 5.23077
20 2QV7 ADP 0.032 0.40501 5.63798
21 1WZ1 DNS 0.04977 0.41395 6.19469
22 2CBZ ATP 0.04275 0.42378 6.75105
23 2J5V PCA 0.01733 0.44012 6.81199
24 4UCC ZKW 0.01537 0.4414 7.29614
25 4WNP 3RJ 0.04079 0.40274 7.31707
26 2OBM ADP 0.02241 0.43446 7.4928
27 3KP6 SAL 0.04991 0.41705 7.94702
28 2IVD ACJ 0.04557 0.40339 9.83264
29 3GC8 B45 0.01207 0.41064 10.8108
30 4HA9 NDP 0.0000001116 0.44826 10.8434
31 5DXV NAP 0.0000000007026 0.49174 32.0513
32 3NRR D16 4.67e-17 0.84377 43.6893
33 3NRR NAP 7.108e-17 0.82023 43.6893
Pocket No.: 3; Query (leader) PDB : 4DP3; Ligand: MMV; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4dp3.bio1) has 43 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4DP3; Ligand: MMV; Similar sites found: 61
This union binding pocket(no: 4) in the query (biounit: 4dp3.bio1) has 45 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1D8C GLV 0.01571 0.43246 1.31579
2 1P7T PYR 0.02644 0.42673 1.31579
3 1YQT ADP 0.0175 0.44044 1.48699
4 1SKQ GDP 0.01942 0.42272 1.6092
5 1LVW TYD 0.0481 0.40545 1.69492
6 2ACV UDP 0.01439 0.42579 1.72786
7 3CV2 COA 0.0142 0.4519 1.8797
8 2IYF UDP 0.04022 0.40003 1.92771
9 2IYA UDP 0.01667 0.41588 2.12264
10 3KYF 5GP 5GP 0.009606 0.44267 2.5974
11 2HHP FLC 0.02967 0.4449 2.64151
12 1WD4 AHR 0.04974 0.40814 2.6971
13 2YVK MRU 0.02711 0.40557 3.125
14 4WOV 3SM 0.03683 0.40824 3.15457
15 2VZ6 FEF 0.02627 0.41951 3.19489
16 2VGD XYP XYP XYP FX3 0.0452 0.40044 3.21101
17 3NHB ADP 0.03029 0.42614 3.26797
18 3B5J 12D 0.03205 0.42261 3.29218
19 1NLM UD1 0.03489 0.40021 3.2967
20 1U5R ATP 0.02563 0.40983 3.44828
21 5GOE GDP 0.0407 0.40279 3.5545
22 1ZGA HMK 0.03372 0.41025 3.64146
23 2VOH CIT 0.01651 0.40909 3.82166
24 5MOB A8S 0.03938 0.41012 3.87931
25 2X1E X1E 0.03437 0.41477 3.92157
26 2F2U M77 0.04358 0.40776 3.9801
27 2NUN ADP 0.03449 0.41689 4.02477
28 1TZJ A3B 0.02295 0.43268 4.14201
29 1MVN FMN 0.01242 0.40481 4.30622
30 4RW3 SHV 0.04358 0.4306 4.63576
31 3B6C SDN 0.01407 0.44255 4.70085
32 4WZ6 ATP 0.03755 0.42084 4.82759
33 2H8H H8H 0.03337 0.40115 4.85981
34 1C3X 8IG 0.04212 0.41482 4.88722
35 4BGB ADP 0.02495 0.42071 5.23077
36 3QDY A2G GAL 0.02722 0.42129 5.59441
37 3QDT A2G GAL 0.02821 0.41939 5.59441
38 2QV7 ADP 0.032 0.40501 5.63798
39 1WZ1 DNS 0.04977 0.41395 6.19469
40 2AWN ADP 0.0177 0.43659 6.29921
41 2ZR9 DTP 0.04551 0.40674 6.59026
42 2CBZ ATP 0.04275 0.42378 6.75105
43 2J5V PCA 0.01733 0.44012 6.81199
44 4UCC ZKW 0.01537 0.4414 7.29614
45 4WNP 3RJ 0.04079 0.40274 7.31707
46 2OBM ADP 0.02241 0.43446 7.4928
47 3NOJ PYR 0.04804 0.40979 7.56302
48 3KP6 SAL 0.04991 0.41705 7.94702
49 1YRB GDP 0.01323 0.42411 8.77863
50 1NJJ ORX 0.02147 0.40197 8.94118
51 1VBO MAN MAN MAN 0.04105 0.41398 9.39597
52 2IVD ACJ 0.04557 0.40339 9.83264
53 1JAY F42 0.04668 0.40615 10.3774
54 3GC8 B45 0.01207 0.41064 10.8108
55 4HA9 NDP 0.0000001116 0.44826 10.8434
56 4F9C 0SX 0.0253 0.41011 11.1111
57 2CK3 ANP 0.0296 0.40086 12
58 4IF4 BEF 0.0483 0.40724 13.9423
59 5DXV NAP 0.0000000007026 0.49174 32.0513
60 3NRR NAP 7.108e-17 0.84806 43.6893
61 3NRR D16 4.67e-17 0.81713 43.6893
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