Receptor
PDB id Resolution Class Description Source Keywords
2D4N 1.53 Å EC: 3.6.1.23 CRYSTAL STRUCTURE OF M-PMV DUTPASE COMPLEXED WITH DUPNPP, SU ANALOGUE MASON-PFIZER MONKEY VIRUS JELLY ROLL HYDROLASE
Ref.: FLEXIBLE SEGMENTS MODULATE CO-FOLDING OF DUTPASE AN NUCLEOCAPSID PROTEINS. NUCLEIC ACIDS RES. V. 35 495 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:999;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
DUP A:777;
Valid;
none;
Kd = 1.2 uM
467.157 C9 H16 N3 O13 P3 C1[C@...
TRS A:1001;
Invalid;
none;
submit data
122.143 C4 H12 N O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2D4N 1.53 Å EC: 3.6.1.23 CRYSTAL STRUCTURE OF M-PMV DUTPASE COMPLEXED WITH DUPNPP, SU ANALOGUE MASON-PFIZER MONKEY VIRUS JELLY ROLL HYDROLASE
Ref.: FLEXIBLE SEGMENTS MODULATE CO-FOLDING OF DUTPASE AN NUCLEOCAPSID PROTEINS. NUCLEIC ACIDS RES. V. 35 495 2007
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 2D4N Kd = 1.2 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 2D4N Kd = 1.2 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 2D4N Kd = 1.2 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DUP; Similar ligands found: 35
No: Ligand ECFP6 Tc MDL keys Tc
1 DUP 1 1
2 DUN 0.816901 1
3 DU 0.742857 0.956522
4 UMP 0.742857 0.956522
5 DUD 0.739726 0.971014
6 DUT 0.701299 0.971014
7 UC5 0.671053 0.957143
8 DUT MG 0.621951 0.876712
9 DUS 0.6 0.820513
10 UMP AF3 PO4 0.595238 0.842105
11 DUR 0.585714 0.842857
12 2KH 0.585366 0.915493
13 UM3 0.506329 0.914286
14 DU DU DU DU BRU DU DU 0.495238 0.831169
15 DDN 0.47561 0.956522
16 DU4 0.472527 0.730769
17 BRU 0.458824 0.891892
18 DDU 0.453333 0.722222
19 DUA 0.450549 0.776316
20 DU3 0.450549 0.773333
21 TYD 0.449438 0.930556
22 UFP 0.447059 0.891892
23 5HU 0.44186 0.930556
24 TMP 0.44186 0.916667
25 5IU 0.436782 0.891892
26 UNP 0.434783 0.915493
27 YYY 0.433333 0.90411
28 UDP 0.431818 0.887324
29 TTP 0.430108 0.930556
30 DC 0.425287 0.890411
31 DCM 0.425287 0.890411
32 UTP 0.417582 0.887324
33 DCP 0.414894 0.90411
34 U5P 0.411765 0.873239
35 BVP 0.408602 0.90411
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2D4N; Ligand: DUP; Similar sites found: 184
This union binding pocket(no: 1) in the query (biounit: 2d4n.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3S9K CIT 0.003017 0.47861 None
2 1UO4 PIH 0.003256 0.4727 None
3 4JCA CIT 0.005833 0.45918 None
4 3KPE TM3 0.002119 0.44992 None
5 2PMP C5P 0.0002938 0.44948 None
6 1YOA FMN 0.01823 0.44102 None
7 1UO5 PIH 0.02958 0.42913 None
8 1PTR PRB 0.01349 0.41895 None
9 1WKL ADP 0.001922 0.40623 None
10 3PMD 11A 0.008749 0.40209 None
11 2QLX RM4 0.03361 0.40006 None
12 4M7F BM3 0.001515 0.44368 1.31579
13 1QH9 LAC 0.01521 0.4109 1.31579
14 1JOT GAL A2G 0.003251 0.41928 1.50376
15 4Q3F TLA 0.003986 0.42061 1.7094
16 1SS4 CIT 0.003204 0.47937 1.97368
17 3EJ0 11X 0.0006448 0.46273 1.97368
18 3NOJ PYR 0.00165 0.44512 1.97368
19 2WIC GNP 0.0001023 0.42972 1.97368
20 1SS4 GSH 0.03597 0.42057 1.97368
21 4BPM GSH 0.0002309 0.41185 1.97368
22 2HMT NAI 0.005167 0.40297 2.08333
23 1OGD RIP 0.01153 0.40617 2.29008
24 3TA2 AKG 0.00003633 0.45225 2.54237
25 3TA2 ATP 0.00204 0.40266 2.54237
26 4DN8 BMA 0.0007274 0.47104 2.63158
27 2XI7 XI7 0.005612 0.46975 2.63158
28 2VJJ RAM GLC GAL NAG NAG GLC 0.0009235 0.43019 2.63158
29 2Q37 3AL 0.004512 0.42904 2.63158
30 2QIA U20 0.003159 0.41413 2.63158
31 3I8T LBT 0.008815 0.41114 2.63158
32 1JAC AMG 0.01707 0.4342 3.00752
33 3ZPG 5GP 0.006342 0.44881 3.28947
34 2X61 CH 0.0004559 0.43082 3.28947
35 2X61 NGA GAL SIA 0.002378 0.42121 3.28947
36 4N02 FNR 0.003971 0.41024 3.28947
37 1EDO NAP 0.008379 0.40832 3.28947
38 3BRE C2E 0.01995 0.4055 3.28947
39 1GSA ADP 0.004934 0.40366 3.28947
40 4LHM AZZ 0.01761 0.40295 3.28947
41 2OFD NGA 0.0004571 0.48021 3.52113
42 2OFE NAG 0.00134 0.45898 3.52113
43 3TKA CTN 0.003126 0.50078 3.94737
44 1H6W SER LEU ASN TYR ILE ILE LYS VAL LYS GLU 0.0001123 0.46193 3.94737
45 4B16 NAG 0.005299 0.4614 3.94737
46 2NLI LAC 0.00131 0.43193 3.94737
47 2NLI FMN 0.001185 0.43193 3.94737
48 1SQ5 ADP 0.002625 0.41821 3.94737
49 3VOZ 04A 0.001438 0.41469 3.94737
50 1SQ5 PAU 0.00824 0.41239 3.94737
51 2BLE 5GP 0.004736 0.41205 3.94737
52 1CBF SAH 0.002486 0.4103 3.94737
53 3KYF 5GP 5GP 0.005716 0.40949 3.94737
54 4G1V FAD 0.01519 0.40942 3.94737
55 4HZD COA 0.001512 0.40877 3.94737
56 3L6R MLI 0.02432 0.40678 3.94737
57 2JBH 5GP 0.01115 0.40217 3.94737
58 3CXO 1N5 0.001955 0.4 3.94737
59 3UEC ALA ARG TPO LYS 0.004381 0.44206 4.10959
60 1JN2 SFP 0.001517 0.52168 4.60526
61 2ZWS PLM 0.006225 0.46723 4.60526
62 2OWZ CIT 0.003527 0.43985 4.60526
63 2WGC SIA GAL BGC 0.01932 0.43959 4.60526
64 1WGC SIA GAL BGC 0.02289 0.42734 4.60526
65 1DXY COI 0.02466 0.41853 4.60526
66 4E28 9MZ 0.01283 0.41428 4.60526
67 1XMV ADP 0.003182 0.41279 4.60526
68 2Q3M MLA 0.03435 0.41107 4.60526
69 2EB5 OXL 0.0153 0.41078 4.60526
70 3L24 GOA 0.03529 0.41047 4.60526
71 1FS5 16G 0.002564 0.40189 4.60526
72 1V6A TRE 0.0202 0.40031 4.60526
73 2DWU DGL 0.01239 0.40029 4.60526
74 1KYQ NAD 0.002898 0.40005 4.60526
75 1BTN I3P 0.001347 0.51455 4.71698
76 2GJ3 FAD 0.0007114 0.41341 5
77 3RF4 FUN 0.0057 0.41921 5.17241
78 2BO4 FLC 0.00372 0.44541 5.26316
79 2YIV YIV 0.006704 0.4401 5.26316
80 4LO6 SIA GAL 0.005915 0.43925 5.26316
81 4O8A 2OP 0.01117 0.43621 5.26316
82 3MB5 SAM 0.002621 0.41489 5.26316
83 2Y7P SAL 0.007575 0.41394 5.26316
84 1V5F FAD 0.02648 0.4132 5.26316
85 1V5F TPP 0.02648 0.4132 5.26316
86 2VQ5 LDP 0.0333 0.41177 5.26316
87 3QV9 QV7 0.01794 0.4026 5.26316
88 1ULE GLA GAL NAG 0.003693 0.45281 5.33333
89 1H8P PC 0.02434 0.41882 5.50459
90 3QDY CBS 0.0008906 0.4747 5.59441
91 1Y2W NAG 0.0005237 0.47752 5.6338
92 1A5Z OXM 0.002219 0.46366 5.92105
93 1B74 DGN 0.003474 0.45411 5.92105
94 1RYI GOA 0.02085 0.43937 5.92105
95 1T26 GBD 0.004767 0.42812 5.92105
96 1T26 NAI 0.004767 0.42812 5.92105
97 4C6F NCD 0.003756 0.41678 5.92105
98 4C6F DOR 0.003756 0.41678 5.92105
99 2XDQ MGX 0.02696 0.41653 5.92105
100 1GJW GLC 0.01619 0.41519 5.92105
101 4RJK PYR 0.03161 0.40685 5.92105
102 1O9U ADZ 0.04544 0.40475 5.92105
103 1JA9 NDP 0.01304 0.4013 5.92105
104 1O7N IND 0.001302 0.40076 5.92105
105 2Q8H TF4 0.003171 0.4642 6.57895
106 4CMF PXG 0.0001165 0.46188 6.57895
107 3PNA CMP 0.001496 0.43814 6.57895
108 3B9Z CO2 0.0049 0.43336 6.57895
109 1XX4 BAM 0.003522 0.43088 6.57895
110 3K3G MMU 0.003677 0.43007 6.57895
111 1H16 PYR 0.01879 0.41806 6.57895
112 3SHR CMP 0.003811 0.41653 6.57895
113 1H16 DTL 0.03771 0.40897 6.57895
114 4HZX G39 0.002573 0.40567 6.57895
115 4F8L GAL 0.03389 0.42578 6.89655
116 2NS1 ADP 0.001771 0.40466 6.89655
117 1NXJ GLV 0.0005193 0.45704 7.23684
118 4LKK SIA GAL 0.0001081 0.44951 7.23684
119 1NXJ TLA 0.000247 0.4444 7.23684
120 4IVG ANP 0.0006519 0.4359 7.23684
121 3W54 RNB 0.002392 0.41522 7.23684
122 3MAG 3MA 0.04121 0.41352 7.23684
123 1F8F NAD 0.003787 0.41254 7.23684
124 1YBH FAD 0.01037 0.41247 7.23684
125 3LTW HLZ 0.01837 0.40715 7.23684
126 4B9E FAH 0.02542 0.40586 7.23684
127 4M51 BEZ 0.04126 0.40108 7.23684
128 3VCA PRO 0.0007482 0.45995 7.89474
129 4TSK NDP 0.001145 0.43246 7.89474
130 1A8S PPI 0.001324 0.43226 7.89474
131 1C0I FAD 0.002666 0.41109 7.89474
132 1C0I BE2 0.002666 0.41109 7.89474
133 4AF5 CIT 0.01711 0.40855 7.89474
134 4OE4 NAD 0.001051 0.40798 7.89474
135 1NU4 MLA 0.001488 0.49083 8.24742
136 1Z6K OAA 0.001059 0.43607 8.55263
137 3F81 STT 0.02244 0.42064 8.55263
138 2IZ1 ATR 0.01563 0.41036 8.55263
139 1RYD GLC 0.01941 0.40605 8.55263
140 2O66 FLC 0.004509 0.42905 8.88889
141 1JQ5 NAD 0.00557 0.4363 9.21053
142 2HVK TBA 0.006639 0.42734 9.21053
143 3FS8 TDR 0.003067 0.4261 9.21053
144 3FS8 ACO 0.00614 0.41677 9.21053
145 1T10 F6P 0.01771 0.40285 9.21053
146 3BY8 MLT 0.0142 0.41789 9.85915
147 1Y1A GSH 0.01842 0.4392 9.86842
148 3R51 MMA 0.01825 0.42527 9.86842
149 1Q3Q ANP 0.003573 0.41343 9.86842
150 4JWX 1N4 0.00966 0.40944 9.86842
151 3FPZ AHZ 0.003131 0.42872 10.5263
152 3H86 AP5 0.001326 0.42734 10.5263
153 3MD0 GDP 0.002989 0.42576 10.5263
154 3I6B KDO 0.01361 0.40309 10.5263
155 2NCD ADP 0.01789 0.40264 10.5263
156 2FGQ MLT 0.0006854 0.47221 11.1842
157 1O6B ADP 0.0002858 0.44327 11.1842
158 4N69 SER 0.002965 0.44328 11.8421
159 4M5P MLA 0.02831 0.42236 11.8421
160 1Y75 NAG 0.01178 0.40119 12.7119
161 4GQB 0XU 0.002618 0.41658 13.1579
162 2YP9 SIA CMO 0.001209 0.41954 13.8158
163 1LDM OXM 0.004376 0.41413 14.4737
164 3Q3C NAD 0.001028 0.43079 15.1316
165 1SC3 MLI 0.01113 0.42928 15.1316
166 2IMP NAI 0.004886 0.42155 15.1316
167 1TV5 ORO 0.001798 0.41331 15.1316
168 1FWE HAE 0.009925 0.40427 15.7895
169 3HZS M0E 0.0004649 0.43282 17.7632
170 5DRN 5CT 0.01741 0.42992 18.4211
171 4OYA 1VE 0.00628 0.42541 18.4211
172 1Z42 HBA 0.001892 0.49931 19.0789
173 1Z44 NPO 0.01562 0.4448 19.0789
174 1I2B USQ 0.01434 0.41865 19.7368
175 1I2B UPG 0.01434 0.41865 19.7368
176 1I2B NAD 0.01434 0.41865 19.7368
177 2BOI MFU 0.004514 0.42352 20.354
178 2QXX TTP 0.00000000002749 0.53729 23.0263
179 3WE0 FAD 0.002217 0.41193 23.0263
180 1QO0 BMD 0.005124 0.43247 24.3421
181 4C2G ALA ALA ALA ALA 0.007502 0.40929 24.3421
182 1RZM E4P 0.007581 0.43081 25
183 3K9W ADE 0.01776 0.40683 25
184 3K9W 4PS 0.01776 0.40683 25
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