Receptor
PDB id Resolution Class Description Source Keywords
1UCD 1.3 Å EC: 3.1.27.1 CRYSTAL STRUCTURE OF RIBONUCLEASE MC1 FROM BITTER GOURD SEEDS COMPLEXED WITH 5'-UMP MOMORDICA CHARANTIA ALPHA PLUS BETA HYDROLASE
Ref.: STRUCTURE OF RNASE MC1 FROM BITTER GOURD SEEDS IN COMPLEX WITH 5'UMP TO BE PUBLISHED
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
U5P A:500;
Valid;
none;
submit data
324.181 C9 H13 N2 O9 P C1=CN...
URA A:501;
Valid;
none;
submit data
112.087 C4 H4 N2 O2 C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1UCD 1.3 Å EC: 3.1.27.1 CRYSTAL STRUCTURE OF RIBONUCLEASE MC1 FROM BITTER GOURD SEEDS COMPLEXED WITH 5'-UMP MOMORDICA CHARANTIA ALPHA PLUS BETA HYDROLASE
Ref.: STRUCTURE OF RNASE MC1 FROM BITTER GOURD SEEDS IN COMPLEX WITH 5'UMP TO BE PUBLISHED
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1UCA - U2P C9 H13 N2 O9 P C1=CN(C(=O....
2 1V9H - U5P C9 H13 N2 O9 P C1=CN(C(=O....
3 1UCC - U3P C9 H13 N2 O9 P C1=CN(C(=O....
4 1J1F - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
5 1UCD - URA C4 H4 N2 O2 C1=CNC(=O)....
6 1J1G - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1UCA - U2P C9 H13 N2 O9 P C1=CN(C(=O....
2 1V9H - U5P C9 H13 N2 O9 P C1=CN(C(=O....
3 1UCC - U3P C9 H13 N2 O9 P C1=CN(C(=O....
4 1J1F - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
5 1UCD - URA C4 H4 N2 O2 C1=CNC(=O)....
6 1J1G - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1UCA - U2P C9 H13 N2 O9 P C1=CN(C(=O....
2 1V9H - U5P C9 H13 N2 O9 P C1=CN(C(=O....
3 1UCC - U3P C9 H13 N2 O9 P C1=CN(C(=O....
4 1J1F - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
5 1UCD - URA C4 H4 N2 O2 C1=CNC(=O)....
6 1J1G - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
7 1IYB - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
8 1VD1 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
9 1VCZ - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
10 1VD3 - U2P C9 H13 N2 O9 P C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: U5P; Similar ligands found: 120
No: Ligand ECFP6 Tc MDL keys Tc
1 U5P 1 1
2 44P 0.790323 0.941176
3 UDP 0.78125 0.984615
4 UTP 0.746269 0.984615
5 2KH 0.735294 0.955224
6 UDP UDP 0.727273 0.953846
7 UPU 0.694444 0.954545
8 UNP 0.690141 0.955224
9 URM 0.662338 0.913043
10 660 0.662338 0.913043
11 URI 0.661017 0.848485
12 U 0.661017 0.848485
13 UFM 0.641026 0.926471
14 GDU 0.641026 0.926471
15 UPG 0.641026 0.926471
16 GUD 0.641026 0.926471
17 U2F 0.6375 0.875
18 UPF 0.6375 0.875
19 Y6W 0.632911 0.875
20 UDH 0.628205 0.851351
21 UPP 0.628205 0.926471
22 UFG 0.617284 0.875
23 CJB 0.603175 0.80597
24 UDX 0.597561 0.926471
25 UAD 0.597561 0.926471
26 UDP GAL 0.597561 0.898551
27 3UC 0.588235 0.875
28 U U 0.585366 0.969697
29 UGB 0.583333 0.940298
30 USQ 0.583333 0.807692
31 UGA 0.583333 0.940298
32 5FU 0.57971 0.927536
33 G3N 0.576471 0.9
34 U3P 0.573529 0.953846
35 UA3 0.573529 0.953846
36 C 0.571429 0.941176
37 CH 0.571429 0.926471
38 CAR 0.571429 0.941176
39 C5P 0.571429 0.941176
40 UDM 0.568182 0.9
41 5BU 0.56338 0.927536
42 U4S 0.557143 0.763889
43 UD1 0.555556 0.913043
44 UD2 0.555556 0.913043
45 CSQ 0.550562 0.863014
46 CSV 0.550562 0.863014
47 U3S 0.541667 0.763889
48 U2S 0.541667 0.777778
49 CNU 0.540541 0.941176
50 S5P 0.535211 0.901408
51 16B 0.534247 0.901408
52 U2P 0.528571 0.939394
53 DU 0.527778 0.911765
54 UMP 0.527778 0.911765
55 HP7 0.526882 0.926471
56 UD7 0.526882 0.913043
57 MJZ 0.521277 0.9
58 UP6 0.521127 0.884058
59 UD4 0.515789 0.9
60 HWU 0.515789 0.887324
61 12V 0.515789 0.887324
62 BMP 0.513889 0.955224
63 UP5 0.510204 0.84
64 DKX 0.507246 0.732394
65 U6M 0.506849 0.969697
66 NUP 0.506849 0.927536
67 IUG 0.505155 0.797468
68 EPZ 0.5 0.9
69 U1S 0.5 0.76
70 JW5 0.5 0.955224
71 4TC 0.5 0.818182
72 EPU 0.49505 0.887324
73 A U 0.49505 0.815789
74 EEB 0.49505 0.887324
75 UDZ 0.494949 0.84
76 H2U 0.486111 0.911765
77 6AU 0.480519 0.969697
78 OMP 0.480519 0.969697
79 6CN 0.480519 0.941176
80 TKW 0.48 0.927536
81 UMF 0.479452 0.869565
82 UUA 0.477612 0.757576
83 U U U U 0.476744 0.954545
84 BMQ 0.472222 0.939394
85 PUP 0.47191 0.926471
86 5HM 0.467532 0.888889
87 O7E 0.463415 0.941176
88 ICR 0.460526 0.830986
89 UMA 0.458716 0.9
90 O7M 0.45679 0.941176
91 UC5 0.455696 0.885714
92 UTP U U U 0.454545 0.909091
93 CDP 0.45 0.927536
94 2TU 0.449275 0.760563
95 FNU 0.441558 0.876712
96 2QR 0.439655 0.810127
97 N3E 0.4375 0.743243
98 DUD 0.4375 0.898551
99 2OM 0.435897 0.925373
100 U22 0.434783 0.777778
101 U21 0.434783 0.797468
102 U20 0.434783 0.797468
103 DUT 0.433735 0.898551
104 CTP 0.433735 0.927536
105 8OP 0.428571 0.849315
106 8GM 0.421687 0.853333
107 5GW 0.420455 0.927536
108 U A A U 0.418803 0.853333
109 4RA 0.414634 0.842105
110 DUP 0.411765 0.873239
111 DUN 0.409639 0.873239
112 CDP MG 0.409639 0.861111
113 UD0 0.408 0.831169
114 UVC 0.407895 0.842857
115 UM3 0.407895 0.897059
116 C5G 0.404255 0.875
117 UPA 0.401869 0.828947
118 A U C C 0.401639 0.794872
119 A G U 0.4 0.7875
120 UAG 0.4 0.851351
Ligand no: 2; Ligand: URA; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 URA 1 1
2 TUL 0.5 0.725
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1UCD; Ligand: U5P; Similar sites found: 26
This union binding pocket(no: 1) in the query (biounit: 1ucd.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2FWP CIT 0.007239 0.4195 None
2 2FWP ICR 0.009428 0.41805 None
3 3FRH SAH 0.01502 0.41987 1.05263
4 4B5P ACO 0.02971 0.40945 1.57895
5 1NF8 BOG 0.01409 0.40704 2.10526
6 5FH7 5XL 0.01064 0.4122 2.41935
7 3OBT SLB 0.004503 0.41072 2.63158
8 2V5E SCR 0.03342 0.40009 3.68421
9 1XKD NAP 0.009005 0.43998 4.21053
10 1TV5 N8E 0.007199 0.42261 4.21053
11 9LDT NAD 0.04932 0.40244 4.21053
12 5V4R MGT 0.001565 0.45479 4.32099
13 4IX4 ADP 0.0141 0.4182 4.73684
14 4N9Z V3L 0.004327 0.43086 5.78947
15 3LCV SAM 0.01845 0.41496 5.78947
16 3AKK ADP 0.02378 0.40254 5.78947
17 4XSU UDP 0.02492 0.41099 6.84211
18 4XSU GLC 0.02935 0.40664 6.84211
19 5G3N X28 0.03126 0.40002 7.87402
20 1X0P FAD 0.01161 0.41499 9.79021
21 3WCA FPS 0.02126 0.41833 12.1053
22 5OCA 9QZ 0.01965 0.40272 15.7895
23 1DCP HBI 0.002688 0.43686 17.3077
24 4RW3 TDA 0.01178 0.40387 17.3684
25 4DW4 U5P 0.00005061 0.52109 18.5629
26 2EA1 GPG 0.00002014 0.48387 18.9474
Pocket No.: 2; Query (leader) PDB : 1UCD; Ligand: URA; Similar sites found: 12
This union binding pocket(no: 2) in the query (biounit: 1ucd.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2IF8 ADP 0.01751 0.40663 None
2 1NF8 BOG 0.02788 0.40704 2.10526
3 1TZD ADP 0.02299 0.40551 3.15789
4 1TV5 N8E 0.01617 0.42079 4.21053
5 5V4R MGT 0.003006 0.45676 4.32099
6 4N9Z V3L 0.008425 0.43086 5.78947
7 5OCA 9QZ 0.03723 0.40243 15.7895
8 1DCP HBI 0.005623 0.43686 17.3077
9 4RW3 TDA 0.0214 0.40387 17.3684
10 2Y69 CHD 0.01584 0.41536 17.4419
11 5W97 CHD 0.01514 0.41368 17.6471
12 4DW4 U5P 0.00022 0.42479 18.5629
Feedback