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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 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[....
50% Homology Family (8)
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[....
7 1IYB - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
8 1VD3 - U2P C9 H13 N2 O9 P C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: U5P; Similar ligands found: 121
No: Ligand ECFP6 Tc MDL keys Tc
1 U 1 1
2 U5P 1 1
3 44P 0.790323 0.941176
4 UDP 0.78125 0.984615
5 UTP 0.746269 0.984615
6 2KH 0.735294 0.955224
7 UDP UDP 0.727273 0.953846
8 UPU 0.694444 0.954545
9 UNP 0.690141 0.955224
10 660 0.662338 0.913043
11 URM 0.662338 0.913043
12 URI 0.661017 0.848485
13 GUD 0.641026 0.926471
14 UFM 0.641026 0.926471
15 UPG 0.641026 0.926471
16 GDU 0.641026 0.926471
17 UPF 0.6375 0.875
18 U2F 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 3UC 0.588235 0.875
27 U U 0.585366 0.969697
28 UGB 0.583333 0.940298
29 USQ 0.583333 0.807692
30 UGA 0.583333 0.940298
31 5FU 0.57971 0.927536
32 G3N 0.576471 0.9
33 UA3 0.573529 0.953846
34 U3P 0.573529 0.953846
35 CAR 0.571429 0.941176
36 C 0.571429 0.941176
37 C5P 0.571429 0.941176
38 UDM 0.568182 0.9
39 5BU 0.56338 0.927536
40 U4S 0.557143 0.763889
41 UD1 0.555556 0.913043
42 UD2 0.555556 0.913043
43 CSQ 0.550562 0.863014
44 CSV 0.550562 0.863014
45 U2S 0.541667 0.777778
46 U3S 0.541667 0.763889
47 CNU 0.540541 0.941176
48 S5P 0.535211 0.901408
49 16B 0.534247 0.901408
50 U2P 0.528571 0.939394
51 DU 0.527778 0.911765
52 UMP 0.527778 0.911765
53 HP7 0.526882 0.926471
54 UD7 0.526882 0.913043
55 MJZ 0.521277 0.9
56 UP6 0.521127 0.884058
57 12V 0.515789 0.887324
58 F5G 0.515789 0.913043
59 UD4 0.515789 0.9
60 HWU 0.515789 0.887324
61 F5P 0.515789 0.9
62 BMP 0.513889 0.955224
63 UP5 0.510204 0.84
64 DKX 0.507246 0.732394
65 NUP 0.506849 0.927536
66 U6M 0.506849 0.969697
67 IUG 0.505155 0.797468
68 EPZ 0.5 0.9
69 U1S 0.5 0.76
70 4TC 0.5 0.818182
71 JW5 0.5 0.955224
72 EEB 0.49505 0.887324
73 A U 0.49505 0.815789
74 EPU 0.49505 0.887324
75 UDZ 0.494949 0.84
76 H2U 0.486111 0.911765
77 OMP 0.480519 0.969697
78 6AU 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 G U 0.471154 0.797468
87 5HM 0.467532 0.888889
88 O7E 0.463415 0.941176
89 ICR 0.460526 0.830986
90 UMA 0.458716 0.9
91 O7M 0.45679 0.941176
92 UC5 0.455696 0.885714
93 UTP U U U 0.454545 0.909091
94 CDP 0.45 0.927536
95 2TU 0.449275 0.760563
96 FNU 0.441558 0.876712
97 2QR 0.439655 0.810127
98 DUD 0.4375 0.898551
99 N3E 0.4375 0.743243
100 2OM 0.435897 0.925373
101 U21 0.434783 0.797468
102 U20 0.434783 0.797468
103 U22 0.434783 0.777778
104 DUT 0.433735 0.898551
105 HF4 0.433735 0.927536
106 CTP 0.433735 0.927536
107 8OP 0.428571 0.849315
108 8GM 0.421687 0.853333
109 5GW 0.420455 0.927536
110 U A A U 0.418803 0.853333
111 4RA 0.414634 0.842105
112 DUP 0.411765 0.873239
113 DUN 0.409639 0.873239
114 UD0 0.408 0.831169
115 UVC 0.407895 0.842857
116 UM3 0.407895 0.897059
117 C5G 0.404255 0.875
118 UPA 0.401869 0.828947
119 A U C C 0.401639 0.794872
120 UAG 0.4 0.851351
121 A G U 0.4 0.7875
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 with APoc: 132
This union binding pocket(no: 1) in the query (biounit: 1ucd.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 4DOO DAO None
2 2FWP CIT None
3 2FWP ICR None
4 3OJF IMJ None
5 4KBS PX2 None
6 4O4F ATP None
7 4O4F IHP None
8 1YRX FMN None
9 1PZO CBT None
10 4B8V NDG NAG NAG NAG None
11 3IQE H4M None
12 3FRH SAH 1.05263
13 3RC1 NAP 1.57895
14 2HQM FAD 1.57895
15 4B5P ACO 1.57895
16 1SC6 NAD 1.57895
17 5D9J 0N8 1.60428
18 1NU4 MLA 2.06186
19 2B4R NAD 2.10526
20 2B4R AES 2.10526
21 1RJW ETF 2.10526
22 5ZZ6 NAD 2.10526
23 4M3P HCS 2.10526
24 1NF8 BOG 2.10526
25 3WCS MAN NAG GAL 2.10526
26 3QLM PLM 2.41935
27 5FH7 5XL 2.41935
28 4Z0H NAD 2.63158
29 3V1Y NAD 2.63158
30 3OBT SLB 2.63158
31 4H6U ACO 2.63158
32 2CDU FAD 3.15789
33 1W2D ADP 3.15789
34 5JBX COA 3.15789
35 1W2D 4IP 3.15789
36 1XA4 COA 3.15789
37 3KP6 SAL 3.31126
38 1D4D FAD 3.68421
39 1Q9I FAD 3.68421
40 1Q9I TEO 3.68421
41 1JAY F42 3.68421
42 6MB9 COA 3.68421
43 6MB9 NMY 3.68421
44 3KJS NAP 3.68421
45 4MO2 FAD 3.68421
46 2DX7 CIT 3.68421
47 4MO2 FDA 3.68421
48 3QMK SGN IDS SGN IDS 3.68421
49 3H8V ATP 3.68421
50 3NTA COA 3.68421
51 1PUJ GNP 3.68421
52 4AZJ SEP PLP 3.68421
53 1W4R TTP 3.68421
54 2V5E SCR 3.68421
55 6GL8 F3Q 4.06977
56 1XKD NAP 4.21053
57 1TV5 N8E 4.21053
58 9LDT NAD 4.21053
59 3MBG FAD 4.31655
60 5V4R MGT 4.32099
61 3QKD HI0 4.41989
62 6GD6 EVB 4.62963
63 5OCQ CIT 4.73684
64 6G14 G4P 4.73684
65 5GLN XYP XYP XYP 4.73684
66 5MW8 ATP 4.73684
67 5N6C NAD 4.73684
68 5IXK 6EW 4.73684
69 4IX4 ADP 4.73684
70 4PQG UDP 4.73684
71 4ZBR NPS 4.73684
72 4ZBR DIF 4.73684
73 3IHG FAD 4.73684
74 2IYG FMN 4.83871
75 2BYC FMN 5.10949
76 3V91 UPG 5.26316
77 6FL8 TIY 5.26316
78 6FL8 ADP 5.26316
79 5T52 A2G 5.26316
80 5T52 NGA 5.26316
81 3UDZ ADP 5.26316
82 3I51 6PL 5.26316
83 4MRP GSH 5.26316
84 5MBC FMN 5.26316
85 4QWT ACD 5.78947
86 2VYN NAD 5.78947
87 5KTQ DCP 5.78947
88 3LCV SAM 5.78947
89 4G6I RS3 5.78947
90 4YRY FAD 5.78947
91 4NE2 SH2 5.78947
92 2B8T THM 5.78947
93 3AI7 TPP 5.78947
94 3AKK ADP 5.78947
95 5UR0 NAD 6.31579
96 3X0V FAD 6.31579
97 5TTJ FAD 6.31579
98 1U26 IHS 6.31579
99 1M13 HYF 6.31579
100 2A92 NAI 6.31579
101 4XSU GLC 6.84211
102 4XSU UDP 6.84211
103 5J6A P46 7.36842
104 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 7.36842
105 5G3N X28 7.87402
106 2D4V NAD 7.89474
107 4XIZ LPP 8.57143
108 1X0P FAD 9.79021
109 3H9E NAD 10
110 4OGQ 7PH 10
111 1TMX HGX 10.5263
112 3RMK BML 12.0482
113 3WCA FPS 12.1053
114 2HJ3 FAD 12.8
115 5JCA FAD 13.1579
116 2VBU CDP 14.7059
117 4IBF 1D5 14.7287
118 5W7B MYR 14.8936
119 2AKO ADP 15.2632
120 5OCA 9QZ 15.7895
121 1DCP HBI 17.3077
122 4RW3 TDA 17.3684
123 2Y69 CHD 17.4419
124 2DYR PGV 17.6471
125 2DYS PGV 17.6471
126 5ZCO PGV 17.6471
127 5Z84 PGV 17.6471
128 5Z84 CHD 17.6471
129 5ZCO CHD 17.6471
130 4DW4 U5P 18.5629
131 2EA1 GPG 18.9474
132 2HFN FMN 19.6078
Pocket No.: 2; Query (leader) PDB : 1UCD; Ligand: URA; Similar sites found with APoc: 28
This union binding pocket(no: 2) in the query (biounit: 1ucd.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 2IF8 ADP None
2 5D9J 0N8 1.60428
3 1NU4 MLA 2.06186
4 1RJW ETF 2.10526
5 4M3P HCS 2.10526
6 1NF8 BOG 2.10526
7 1TZD ADP 3.15789
8 3KP6 SAL 3.31126
9 5NTP 98E 3.68421
10 3ZQE DXC 4.21053
11 1TV5 N8E 4.21053
12 5V4R MGT 4.32099
13 5OCQ CIT 4.73684
14 5GLN XYP XYP XYP 4.73684
15 5KTQ DCP 5.78947
16 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 7.36842
17 5LX9 OLB 7.89474
18 1RM6 PCD 11.5789
19 5W7B MYR 14.8936
20 5OCA 9QZ 15.7895
21 1DCP HBI 17.3077
22 4RW3 TDA 17.3684
23 2Y69 CHD 17.4419
24 5ZCO CHD 17.6471
25 5W97 CHD 17.6471
26 5Z84 CHD 17.6471
27 4DW4 U5P 18.5629
28 2EA1 GPG 18.9474
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