Receptor
PDB id Resolution Class Description Source Keywords
4DKB 1.83 Å EC: 3.6.1.23 CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI DUTPASE WITH DUPNP A TRYPANOSOMA BRUCEI ALL ALPHA NTP PYROPHOSPHOHYDROLASE ALL ALPHA NTP PYROPHOSPHHYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: ON THE CATALYTIC MECHANISM OF DIMERIC DUTPASES. BIOCHEM.J. V. 456 81 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:302;
A:301;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
DUN A:303;
Valid;
none;
submit data
387.177 C9 H15 N3 O10 P2 C1[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4DL8 1.7 Å EC: 3.6.1.23 CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI DUTPASE WITH DUMP, P [ALF3-OPO3] TRANSITION STATE ANALOGUE, MG2+, AND NA+ TRYPANOSOMA BRUCEI ALL ALPHA NTP PYROPHOSPHOHYDROLASE ALL ALPHA NTP PYROPHOSPHHYDROLASE
Ref.: ON THE CATALYTIC MECHANISM OF DIMERIC DUTPASES. BIOCHEM.J. V. 456 81 2013
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 4DK4 - DUN C9 H15 N3 O10 P2 C1[C@@H]([....
2 4DLC - UMP C9 H13 N2 O8 P C1[C@@H]([....
3 4DL8 - UMP AF3 PO4 n/a n/a
4 4DKB - DUN C9 H15 N3 O10 P2 C1[C@@H]([....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 4DK4 - DUN C9 H15 N3 O10 P2 C1[C@@H]([....
2 4DLC - UMP C9 H13 N2 O8 P C1[C@@H]([....
3 4DL8 - UMP AF3 PO4 n/a n/a
4 4DKB - DUN C9 H15 N3 O10 P2 C1[C@@H]([....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 2CJE - DUN C9 H15 N3 O10 P2 C1[C@@H]([....
2 2YB0 Kd = 140 uM DUR C9 H12 N2 O5 C1[C@@H]([....
3 2YAZ Kd = 7.3 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
4 2YAY Kd = 0.8 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
5 4DK4 - DUN C9 H15 N3 O10 P2 C1[C@@H]([....
6 4DLC - UMP C9 H13 N2 O8 P C1[C@@H]([....
7 4DL8 - UMP AF3 PO4 n/a n/a
8 4DKB - DUN C9 H15 N3 O10 P2 C1[C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DUN; Similar ligands found: 31
No: Ligand ECFP6 Tc MDL keys Tc
1 DUN 1 1
2 DUP 0.816901 1
3 UMP 0.75 0.956522
4 DU 0.75 0.956522
5 DUD 0.69863 0.971014
6 UC5 0.69863 0.957143
7 DUT 0.662338 0.971014
8 DUS 0.625 0.820513
9 DUT MG 0.625 0.876712
10 UMP AF3 PO4 0.617284 0.842105
11 DUR 0.588235 0.842857
12 DU DU DU DU BRU DU DU 0.509804 0.831169
13 UM3 0.506494 0.914286
14 DDN 0.475 0.956522
15 DDU 0.472222 0.722222
16 DUA 0.465909 0.776316
17 UNP 0.465909 0.915493
18 DU3 0.465909 0.773333
19 2KH 0.45977 0.915493
20 BRU 0.457831 0.891892
21 DU4 0.455556 0.730769
22 UFP 0.445783 0.891892
23 5HU 0.440476 0.930556
24 TMP 0.440476 0.916667
25 5IU 0.435294 0.891892
26 DCM 0.423529 0.890411
27 DC 0.423529 0.890411
28 TYD 0.41573 0.930556
29 U5P 0.409639 0.873239
30 BVP 0.406593 0.90411
31 YYY 0.4 0.90411
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4DL8; Ligand: UMP AF3 PO4; Similar sites found: 171
This union binding pocket(no: 1) in the query (biounit: 4dl8.bio1) has 43 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.0003018 0.53365 None
2 1UO4 PIH 0.001183 0.48957 None
3 2BOI MFU 0.001917 0.43293 None
4 1NU4 MLA 0.02747 0.41765 None
5 4LIT AKG 0.003656 0.4269 1.03448
6 3E5P PPI 0.01046 0.45053 1.72414
7 2JC9 ADN 0.001477 0.43765 1.72414
8 2YIV NBN 0.0101 0.41912 1.72414
9 2ZJ5 ADP 0.005815 0.4182 1.72414
10 1FBL HTA 0.006562 0.40115 1.72414
11 1T3D CYS 0.01539 0.41061 1.7301
12 4K30 NLG 0.008208 0.4066 1.875
13 1WRA PC 0.006771 0.4272 2.06897
14 1VBH PEP 0.005699 0.41858 2.06897
15 3ZPG 5GP 0.02187 0.41573 2.06897
16 2Q8H TF4 0.02992 0.41485 2.06897
17 2Z9V PXM 0.005607 0.41351 2.06897
18 4IHQ ADP 0.008063 0.40213 2.06897
19 1Y7P RIP 0.009533 0.42678 2.24215
20 4BT5 23B 0.004482 0.41243 2.33463
21 1B74 DGN 0.003126 0.45015 2.3622
22 1Z42 HBA 0.01633 0.44035 2.41379
23 1H2M OGA 0.003191 0.43562 2.41379
24 2Y0I AKG 0.004458 0.42318 2.41379
25 3P3N AKG 0.007677 0.41858 2.41379
26 1AUA BOG 0.004538 0.41734 2.41379
27 1CKN GTP 0.00566 0.40834 2.41379
28 5EQU AKG 0.02345 0.40782 2.41379
29 3U1T MLI 0.0199 0.40539 2.41379
30 4USS GSH 0.008893 0.40514 2.41379
31 2WA4 069 0.004808 0.40196 2.41379
32 3SCH TB6 0.005004 0.4269 2.52525
33 1ZZ7 S0H 0.008607 0.40574 2.52525
34 2ZO9 MLI 0.004963 0.40363 2.55474
35 1QH9 LAC 0.006885 0.4207 2.58621
36 3PMA SCR 0.002021 0.43198 2.7027
37 4EXO PYR 0.01442 0.41808 2.73973
38 3QP4 HL0 0.001637 0.41048 2.74725
39 1Z45 GAL 0.001426 0.43829 2.75862
40 2OWZ CIT 0.002944 0.43719 2.75862
41 3DGB MUC 0.0008829 0.42985 2.75862
42 2YKX AKG 0.0124 0.41497 2.75862
43 3NNF AKG 0.01074 0.41205 2.75862
44 3SIX GDP 0.002853 0.41056 2.75862
45 2D5X L35 0.006423 0.41633 2.83688
46 2WGC SIA GAL BGC 0.005498 0.46424 2.92398
47 1WGC SIA GAL BGC 0.01128 0.43811 2.92398
48 2VQ5 HBA 0.01031 0.4187 2.98507
49 2VQ5 LDP 0.03131 0.4078 2.98507
50 2BZ1 TAU 0.02376 0.42905 3.06122
51 3UBW 6SP 0.0001313 0.58601 3.06513
52 1RZM E4P 0.005723 0.43059 3.10345
53 1ZED PNP 0.00746 0.42524 3.10345
54 4W6Z ETF 0.01697 0.4213 3.10345
55 1YOE RIB 0.005676 0.40829 3.10345
56 2P69 PLP 0.0107 0.40676 3.10345
57 1M1B SPV 0.01091 0.4064 3.10345
58 1YOA FMN 0.007741 0.45604 3.14465
59 1W3R PYR 0.002079 0.45868 3.24074
60 3L6R MLI 0.006024 0.42955 3.44828
61 4NAO AKG 0.008686 0.42217 3.44828
62 3RF4 FUN 0.004657 0.41687 3.44828
63 4RJK PYR 0.01604 0.41584 3.44828
64 1OIK AKG 0.01626 0.40397 3.44828
65 1Y9Q MED 0.009034 0.41542 3.64583
66 4AF5 CIT 0.006284 0.42247 3.68421
67 3EW2 BTN 0.005571 0.40862 3.7037
68 2ZJF BSU 0.001284 0.42884 3.7931
69 3SQG COM 0.0206 0.42428 3.7931
70 2P41 G1G 0.00288 0.42018 3.7931
71 1GJW GLC 0.01054 0.41826 3.7931
72 1GJW MAL 0.005141 0.4053 3.7931
73 3O03 GCO 0.04009 0.40232 3.7931
74 4HZO COA 0.01151 0.40046 3.7931
75 1JN2 SFP 0.03043 0.42207 3.79747
76 1Y1A GSH 0.04861 0.40797 3.82514
77 1KNY KAN 0.03204 0.40435 3.95257
78 3I7S PYR 0.00635 0.4353 4.13793
79 4ME6 ADP 0.003081 0.4301 4.13793
80 3HP9 CF1 0.01631 0.41738 4.13793
81 3BRE C2E 0.009471 0.4145 4.13793
82 2BO4 FLC 0.01932 0.40599 4.13793
83 1S2D ADE 0.002591 0.40763 4.19162
84 1TUV VK3 0.003997 0.45294 4.38596
85 2WCI GSH 0.01128 0.40576 4.44444
86 2CW6 3HG 0.005478 0.44606 4.48276
87 3IHB TRS 0.01537 0.43348 4.48276
88 4WBD CIT 0.0139 0.41885 4.48276
89 3IHB GLU 0.01341 0.4134 4.48276
90 1F1V DHY 0.008415 0.40138 4.48276
91 1JAC AMG 0.02965 0.41589 4.51128
92 3DX5 DHB 0.004579 0.40727 4.54545
93 1N9L FMN 0.001125 0.40769 4.58716
94 3TKA CTN 0.004477 0.46535 4.61095
95 3LTW HLZ 0.008641 0.41628 4.64286
96 1HQL GLA MBG 0.02012 0.40517 4.66926
97 9LDB OXM 0.0006265 0.50405 4.82759
98 9LDT OXM 0.000648 0.50328 4.82759
99 3L24 GOA 0.007694 0.43863 4.82759
100 4M5P MLA 0.01504 0.43152 4.82759
101 1H16 PYR 0.01379 0.41902 4.82759
102 2PP3 LGT 0.00157 0.41563 4.82759
103 1B5E DCM 0.004374 0.41286 4.87805
104 4A6F SEP 0.003735 0.46336 5
105 3ZVS MLI 0.01109 0.41922 5
106 1PX8 XYP 0.003517 0.42762 5.17241
107 5D63 FUC GAL GLA 0.008617 0.40096 5.17241
108 1U3I GSH 0.007097 0.41446 5.21327
109 1ULE GLA GAL NAG 0.002821 0.45229 5.33333
110 1DXY COI 0.005152 0.4474 5.51724
111 2VDJ HSE 0.01378 0.41904 5.51724
112 1HFA PIO 0.000005576 0.69478 5.53633
113 2OFD NGA 0.01336 0.4078 5.6338
114 4N7C AEF 0.002415 0.44795 5.68182
115 3BHO B4P 0.01041 0.43995 5.76923
116 2XRH NIO 0.006728 0.42732 6
117 2IYG FMN 0.001251 0.42412 6.45161
118 1RYI GOA 0.001595 0.49714 6.55172
119 1I0Z OXM 0.001033 0.48244 6.55172
120 2F2U M77 0.001325 0.42831 6.55172
121 2ZWS PLM 0.03228 0.42163 6.55172
122 2CE7 ADP 0.003425 0.40317 6.55172
123 2YD6 FLC 0.005687 0.45909 6.60377
124 1NF8 BOG 0.005182 0.43259 6.76329
125 1O9U ADZ 0.004738 0.44923 6.89655
126 4O8A 2OP 0.009192 0.43474 6.89655
127 1WTC ACP 0.009267 0.42086 6.89655
128 2OKK ABU 0.01268 0.42079 6.89655
129 3QDV A2G 0.02022 0.41744 6.99301
130 3QDW NDG 0.0148 0.4114 6.99301
131 3QDY CBS 0.01611 0.40969 6.99301
132 3QDT A2G GAL 0.02655 0.40519 6.99301
133 3ZGE ASP 0.006226 0.43571 7.24138
134 3AYS CT3 0.002941 0.41478 7.24138
135 1Q3P GLU ALA GLN THR ARG LEU 0.006327 0.40638 7.33945
136 1WDA BAG 0.001404 0.43276 7.58621
137 4M51 BEZ 0.001869 0.4609 7.93103
138 3O2K DST 0.005372 0.41428 7.93103
139 1FIQ FAD 0.004528 0.40291 7.93103
140 2XDQ MGX 0.01143 0.42997 8.27586
141 1Y75 NAG 0.003345 0.41756 8.47458
142 2ZE3 AKG 0.00836 0.41139 8.72727
143 1NXJ GLV 0.008956 0.40028 8.74317
144 3WUC GLC GAL 0.01535 0.41065 8.75912
145 3MAG 3MA 0.005919 0.45286 8.96552
146 3MCT 3MC 0.001612 0.43607 8.96552
147 1KTC NGA 0.007183 0.40902 8.96552
148 1SS4 GSH 0.01087 0.44875 9.15033
149 1H8P PC 0.03364 0.40621 9.17431
150 1XX4 BAM 0.01172 0.42942 9.1954
151 2Y7G AAE 0.0004224 0.4315 9.21986
152 1KC7 PPR 0.004901 0.43371 9.31034
153 3S9K CIT 0.02752 0.41875 9.32203
154 1JGS SAL 0.01284 0.44389 9.42029
155 3WUD GLC GAL 0.02256 0.40864 9.55882
156 4F8L GAL 0.04291 0.41469 9.65517
157 2QGI UDP 0.00754 0.41333 9.67742
158 3F81 STT 0.02494 0.41283 9.83607
159 3KMT SAH 0.001606 0.41527 10.084
160 1ECM TSA 0.002531 0.42244 10.0917
161 1T0S BML 0.02134 0.40981 10.4651
162 1NP0 NGT 0.01564 0.40472 10.7884
163 2QLX RM4 0.01123 0.41698 11.1111
164 3I0O SMI 0.025 0.40247 13.7931
165 2V5E SCR 0.00579 0.45336 13.8614
166 2VKL MLT 0.03979 0.40907 15.5556
167 2X2T GAL NGA 0.02349 0.41415 15.6863
168 3CBG FER 0.02042 0.41723 15.9483
169 1Y13 BIO 0.003443 0.41211 16.0221
170 4Q3F TLA 0.01373 0.40726 18.8034
171 1BTN I3P 0.009634 0.45503 19.8113
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