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Receptor
PDB id Resolution Class Description Source Keywords
1J1F 1.6 Å EC: 3.1.27.1 CRYSTAL STRUCTURE OF THE RNASE MC1 MUTANT N71T IN COMPLEX WI MOMORDICA CHARANTIA HYDROLASE NUCLEIC ACID RNA
Ref.: CRYSTAL STRUCTURES OF THE RIBONUCLEASE MC1 MUTANTS N71S IN COMPLEX WITH 5'-GMP: STRUCTURAL BASIS FOR ALTERATIONS IN SUBSTRATE SPECIFICITY BIOCHEMISTRY V. 42 5270 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5GP A:295;
Valid;
none;
submit data
363.221 C10 H14 N5 O8 P c1nc2...
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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: 5GP; Similar ligands found: 159
No: Ligand ECFP6 Tc MDL keys Tc
1 G 1 1
2 5GP 1 1
3 GDP 0.828947 0.986486
4 GP3 0.815789 0.960526
5 GP2 0.805195 0.948052
6 GTP 0.797468 0.986486
7 GNH 0.794872 0.973333
8 G2P 0.777778 0.948052
9 GMV 0.775 0.960526
10 G1R 0.765432 0.973333
11 GCP 0.765432 0.960526
12 GAV 0.759036 0.948052
13 GSP 0.756098 0.935897
14 GNP 0.756098 0.960526
15 9GM 0.756098 0.960526
16 ALF 5GP 0.753086 0.9
17 GMP 0.732394 0.866667
18 GPG 0.724138 0.948052
19 G2R 0.712644 0.948052
20 ALF GDP 0.701149 0.9
21 GDP ALF 0.701149 0.9
22 GDP AF3 0.701149 0.9
23 GKE 0.692308 0.948052
24 Y9Z 0.692308 0.890244
25 GDC 0.692308 0.948052
26 GDD 0.692308 0.948052
27 YGP 0.681319 0.9125
28 G3A 0.677419 0.960526
29 G5P 0.670213 0.960526
30 GFB 0.666667 0.948052
31 GDR 0.666667 0.948052
32 GTG 0.666667 0.924051
33 6CK 0.659574 0.924051
34 3GP 0.65 0.959459
35 G G 0.648936 0.960526
36 GKD 0.645833 0.948052
37 JB2 0.645833 0.948052
38 GDX 0.639175 0.960526
39 GPD 0.639175 0.9125
40 GDP 7MG 0.635417 0.923077
41 G3D 0.617977 0.972973
42 U2G 0.617647 0.924051
43 2GP 0.609756 0.946667
44 IMP 0.609756 0.972603
45 JB3 0.607843 0.935897
46 CG2 0.605769 0.924051
47 G4P 0.604396 0.972973
48 DGP 0.60241 0.922078
49 DG 0.60241 0.922078
50 FEG 0.601942 0.890244
51 NGD 0.601942 0.948052
52 ZGP 0.596154 0.879518
53 0O2 0.595745 0.972973
54 2MD 0.584906 0.879518
55 G7M 0.583333 0.960526
56 CAG 0.583333 0.869048
57 G A A A 0.579439 0.935065
58 A G 0.579439 0.947368
59 U A G G 0.574074 0.947368
60 MGD 0.568807 0.879518
61 DBG 0.566372 0.935897
62 PGD 0.5625 0.9125
63 MD1 0.5625 0.879518
64 P2G 0.55814 0.894737
65 GCP G 0.556701 0.933333
66 FE9 0.553571 0.784946
67 P1G 0.545455 0.883117
68 GH3 0.542553 0.96
69 TPG 0.53913 0.829545
70 GPX 0.53125 0.933333
71 DGI 0.527473 0.910256
72 G1R G1R 0.525862 0.911392
73 G U 0.522936 0.911392
74 PGD O 0.521368 0.83908
75 DGT 0.521277 0.910256
76 G4M 0.520325 0.869048
77 AKW 0.513761 0.878049
78 G C 0.513514 0.911392
79 93A 0.511364 0.821429
80 IDP 0.505495 0.959459
81 MGQ 0.505155 0.948052
82 C2R 0.5 0.893333
83 A 0.5 0.905405
84 AMZ 0.5 0.905405
85 BGO 0.5 0.911392
86 AMP 0.5 0.905405
87 AIR 0.493671 0.890411
88 MGV 0.49 0.901235
89 SGP 0.488889 0.8375
90 NIA 0.488095 0.8375
91 GPC 0.474138 0.890244
92 G G G RPC 0.473684 0.886076
93 GGM 0.473684 0.888889
94 71V 0.47191 0.85
95 APC G U 0.470085 0.897436
96 R5I 0.46875 0.933333
97 R7I 0.46875 0.933333
98 MGP 0.46875 0.948052
99 35G 0.468085 0.945946
100 PCG 0.468085 0.945946
101 C2E 0.468085 0.933333
102 G1G 0.466102 0.9125
103 AAM 0.465909 0.905405
104 RMB 0.465909 0.813333
105 FAI 0.465909 0.905405
106 7RA 0.465909 0.918919
107 1RB 0.465116 0.824324
108 6G0 0.463918 0.948052
109 5GP 5GP 0.463158 0.894737
110 G G G C 0.462185 0.924051
111 RBZ 0.45977 0.815789
112 UCG 0.459016 0.923077
113 A G C C 0.458333 0.923077
114 DG DG 0.456311 0.876543
115 G U34 0.45614 0.9
116 IMO 0.449438 0.866667
117 A G U 0.446154 0.9
118 G C C C 0.443548 0.935897
119 IRN 0.443038 0.808219
120 PMO 0.43956 0.792208
121 7RP 0.438202 0.864865
122 GTA 0.436364 0.924051
123 JLN 0.433333 0.88
124 P2P 0.433333 0.842105
125 A G U U 0.42963 0.9
126 XMP 0.428571 0.907895
127 PGS 0.425532 0.804878
128 RVP 0.423529 0.84
129 G2Q 0.423077 0.948052
130 ADP 0.419355 0.906667
131 ABM 0.417582 0.857143
132 A2D 0.417582 0.881579
133 PRT 0.416667 0.945946
134 GUO 0.415842 0.932432
135 AT4 0.414894 0.871795
136 CA0 0.410526 0.883117
137 2SA 0.41 0.871795
138 1YD 0.409091 0.933333
139 4BW 0.409091 0.933333
140 A12 0.408602 0.871795
141 AP2 0.408602 0.871795
142 BA3 0.408602 0.881579
143 6C6 0.408163 0.825
144 25A 0.407767 0.906667
145 NOS 0.406977 0.813333
146 HEJ 0.40625 0.906667
147 ATP 0.40625 0.906667
148 AP5 0.404255 0.881579
149 B4P 0.404255 0.881579
150 ACQ 0.40404 0.883117
151 6IA 0.40404 0.785714
152 ANP 0.40404 0.883117
153 CGP 0.403361 0.878049
154 APC 0.402062 0.871795
155 3ZE 0.402062 0.871795
156 5FA 0.402062 0.906667
157 AQP 0.402062 0.906667
158 N6P 0.4 0.853333
159 AN2 0.4 0.894737
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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