Receptor
PDB id Resolution Class Description Source Keywords
6LOY 1.35 Å EC: 3.2.2.22 CRYSTAL STRUCTURE OF ALPHA-MOMORCHARIN IN COMPLEX WITH DAMP MOMORDICA CHARANTIA ALPHA-MOMORCHARIN RIBOSOME-INACTIVATING PROTEIN RRNA N-GLYDAMP PLANT PROTEIN
Ref.: ATOMIC-RESOLUTION STRUCTURES OF TYPE I RIBOSOME INA PROTEIN ALPHA-MOMORCHARIN WITH DIFFERENT SUBSTRATE INT.J.BIOL.MACROMOL. V. 164 265 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
D5M A:301;
 Valid;
 none;
 submit data
331.222 C10 H14 N5 O6 P c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6LOZ 1.08 Å EC: 3.2.2.22 CRYSTAL STRUCTURE OF ALPHA-MOMORCHARIN IN COMPLEX WITH ADENI MOMORDICA CHARANTIA ALPHA-MOMORCHARIN RIBOSOME-INACTIVATING PROTEIN RRNA N-GLYADENINE PLANT PROTEIN
Ref.: ATOMIC-RESOLUTION STRUCTURES OF TYPE I RIBOSOME INA PROTEIN ALPHA-MOMORCHARIN WITH DIFFERENT SUBSTRATE INT.J.BIOL.MACROMOL. V. 164 265 2020
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 6LOW - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
2 6LOZ - ADE C5 H5 N5 c1[nH]c2c(....
3 6LP0 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
4 6LOY - D5M C10 H14 N5 O6 P c1nc(c2c(n....
5 1MRH - FMC C10 H13 N5 O4 c1nc2c(c(n....
6 6LOQ - CMP C10 H12 N5 O6 P c1nc(c2c(n....
7 6LOV - 4UO C10 H12 N4 O6 c1nc2c(n1[....
8 1MRG - ADN C10 H13 N5 O4 c1nc(c2c(n....
9 6LOR - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
70% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 6LOW - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
2 6LOZ - ADE C5 H5 N5 c1[nH]c2c(....
3 6LP0 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
4 6LOY - D5M C10 H14 N5 O6 P c1nc(c2c(n....
5 1MRH - FMC C10 H13 N5 O4 c1nc2c(c(n....
6 6LOQ - CMP C10 H12 N5 O6 P c1nc(c2c(n....
7 6LOV - 4UO C10 H12 N4 O6 c1nc2c(n1[....
8 1MRG - ADN C10 H13 N5 O4 c1nc(c2c(n....
9 6LOR - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
10 1MRK - FMC C10 H13 N5 O4 c1nc2c(c(n....
11 1QD2 - ADE C5 H5 N5 c1[nH]c2c(....
12 1TCS - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
13 1MRJ - ADN C10 H13 N5 O4 c1nc(c2c(n....
14 1NLI Kd = 260 uM ADE C5 H5 N5 c1[nH]c2c(....
15 1GIS - DA C10 H14 N5 O6 P c1nc(c2c(n....
16 1AHB - FMP C10 H14 N5 O7 P c1nc2c(c(n....
17 1AHA - ADE C5 H5 N5 c1[nH]c2c(....
18 3N1N - GUN C5 H5 N5 O c1[nH]c2c(....
19 3V2K - ADE C5 H5 N5 c1[nH]c2c(....
20 3RL9 - ADE C5 H5 N5 c1[nH]c2c(....
21 3SJ6 - RIP C5 H10 O5 C1[C@H]([C....
22 3U6Z - ADE C5 H5 N5 c1[nH]c2c(....
50% Homology Family (60)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 5DDZ - ASP ASP ASP MET GLY PHE GLY LEU PHE ASP n/a n/a
2 4MX5 ic50 = 28 uM 5MX C17 H17 N7 O4 c1ccc(cc1)....
3 4HV7 ic50 = 300 uM 19J C11 H11 N7 O5 c1c(nc2c(n....
4 3PX8 ic50 = 230 uM JP2 C7 H5 N5 O3 c1c(nc2c(n....
5 5GU4 Kd = 3.4 uM ASP ASP MET GLY PHE GLY LEU PHE ASP n/a n/a
6 1BR6 Ki = 0.6 mM PT1 C14 H12 N6 O3 c1cc(ccc1C....
7 4ESI ic50 = 70 uM 0RB C10 H9 N9 O2 c1c([nH]nn....
8 4HV3 ic50 = 115 uM 19L C21 H20 N8 O6 c1ccc2c(c1....
9 1BR5 Ki > 2 mM NEO C9 H11 N5 O4 c1c(nc2c(n....
10 3EJ5 ic50 = 0.27 mM EJ5 C14 H15 N3 O4 c1cc(ccc1C....
11 4MX1 ic50 = 209 uM 1MX C16 H16 N8 O3 c1ccc(cc1)....
12 3PX9 ic50 = 380 uM JP3 C12 H10 N6 O3 c1cc(oc1)C....
13 4HUO ic50 = 20 uM RS8 C18 H17 N7 O5 c1ccc(cc1)....
14 2P8N Kd = 0.7 mM ADE C5 H5 N5 c1[nH]c2c(....
15 1J1M - GLC GLC n/a n/a
16 4Q2V - 0XE C21 H18 O11 c1ccc(cc1)....
17 6URY ic50 = 400 uM R6T C14 H9 N O2 c1ccc2c(c1....
18 4HUP ic50 = 15 uM 19M C27 H26 N8 O6 c1ccc(cc1)....
19 1IFS - ADE C5 H5 N5 c1[nH]c2c(....
20 1IFU - FMC C10 H13 N5 O4 c1nc2c(c(n....
21 3HIO - C2X C51 H72 N21 O29 P5 CO[C@@H]1[....
22 6URX ic50 = 181 uM JMG C11 H8 O2 S c1ccc(cc1)....
23 2PJO Kd = 900 mM NMU C2 H6 N2 O CNC(=O)N
24 2R3D Kd = 1.4 M ACM C2 H5 N O CC(=O)N
25 6URW ic50 = 32 uM R7T C12 H10 O2 S c1cc(sc1)C....
26 6LOZ - ADE C5 H5 N5 c1[nH]c2c(....
27 6LP0 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
28 6LOY - D5M C10 H14 N5 O6 P c1nc(c2c(n....
29 1MRH - FMC C10 H13 N5 O4 c1nc2c(c(n....
30 6LOQ - CMP C10 H12 N5 O6 P c1nc(c2c(n....
31 6LOV - 4UO C10 H12 N4 O6 c1nc2c(n1[....
32 1MRG - ADN C10 H13 N5 O4 c1nc(c2c(n....
33 6LOR - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
34 3KU0 - ADE C5 H5 N5 c1[nH]c2c(....
35 2QET - ADE C5 H5 N5 c1[nH]c2c(....
36 1LPC - CMP C10 H12 N5 O6 P c1nc(c2c(n....
37 1GIU - ADE C5 H5 N5 c1[nH]c2c(....
38 1MRK - FMC C10 H13 N5 O4 c1nc2c(c(n....
39 1QD2 - ADE C5 H5 N5 c1[nH]c2c(....
40 1TCS - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
41 1MRJ - ADN C10 H13 N5 O4 c1nc(c2c(n....
42 1NLI Kd = 260 uM ADE C5 H5 N5 c1[nH]c2c(....
43 1GIS - DA C10 H14 N5 O6 P c1nc(c2c(n....
44 1AHB - FMP C10 H14 N5 O7 P c1nc2c(c(n....
45 1AHA - ADE C5 H5 N5 c1[nH]c2c(....
46 3N1N - GUN C5 H5 N5 O c1[nH]c2c(....
47 3V2K - ADE C5 H5 N5 c1[nH]c2c(....
48 3RL9 - ADE C5 H5 N5 c1[nH]c2c(....
49 3SJ6 - RIP C5 H10 O5 C1[C@H]([C....
50 3U6Z - ADE C5 H5 N5 c1[nH]c2c(....
51 1J1S - FMP C10 H14 N5 O7 P c1nc2c(c(n....
52 1D6A - GUN C5 H5 N5 O c1[nH]c2c(....
53 1QCJ - APT C14 H13 N6 O3 c1cc(ccc1C....
54 1QCI - ADE C5 H5 N5 c1[nH]c2c(....
55 3LE7 - ADE C5 H5 N5 c1[nH]c2c(....
56 5Z3J - NCA C6 H6 N2 O c1cc(cnc1)....
57 5Z3I - ADE C5 H5 N5 c1[nH]c2c(....
58 3HIW Ki = 3.9 nM C2X C51 H72 N21 O29 P5 CO[C@@H]1[....
59 3HIV Ki = 7.5 nM TXN C37 H52 N15 O20 P3 CO[C@@H]1[....
60 3HIT Ki = 6.4 nM DYN C30 H47 N10 O17 P3 CO[C@@H]1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: D5M; Similar ligands found: 158
No: Ligand ECFP6 Tc MDL keys Tc
1 DA 1 1
2 D5M 1 1
3 DAT 0.816901 0.971831
4 AS 0.808824 0.945205
5 DTP 0.773333 0.971831
6 DZ4 0.763158 0.945205
7 3D1 0.707692 0.833333
8 3L1 0.707692 0.833333
9 DOI 0.68 0.916667
10 6MA 0.68 0.957747
11 5F1 0.661765 0.816901
12 101 0.613333 0.943662
13 CPA 0.585859 0.860759
14 7D5 0.581081 0.890411
15 6OG 0.580247 0.932432
16 103 0.578947 0.849315
17 AMP 0.558442 0.902778
18 A 0.558442 0.902778
19 A3P 0.54321 0.902778
20 DDS 0.528736 0.916667
21 A2P 0.52439 0.915493
22 CUU 0.517647 0.90411
23 DG 0.511905 0.894737
24 DGP 0.511905 0.894737
25 HF7 0.511111 0.958333
26 ZDA 0.505747 0.826667
27 ABM 0.5 0.853333
28 45A 0.5 0.853333
29 3AT 0.494382 0.90411
30 7D3 0.493976 0.866667
31 ADP 0.482353 0.878378
32 A2D 0.481928 0.853333
33 KF5 0.479452 0.652778
34 V3L 0.477778 0.878378
35 DI 0.476744 0.893333
36 AMP MG 0.47561 0.863014
37 2AM 0.475 0.902778
38 PPS 0.472527 0.792683
39 PAP 0.47191 0.890411
40 ADX 0.471264 0.771084
41 7D4 0.471264 0.866667
42 BA3 0.470588 0.853333
43 A12 0.470588 0.893333
44 AP2 0.470588 0.893333
45 3AM 0.469136 0.888889
46 MDR 0.467532 0.780822
47 ATP 0.465909 0.878378
48 HEJ 0.465909 0.878378
49 B4P 0.465116 0.853333
50 AP5 0.465116 0.853333
51 AQP 0.460674 0.878378
52 APC 0.460674 0.893333
53 PRX 0.460674 0.855263
54 2A5 0.460674 0.905405
55 5FA 0.460674 0.878378
56 3AD 0.460526 0.791667
57 AT4 0.45977 0.844156
58 AN2 0.45977 0.866667
59 J4G 0.459184 0.881579
60 OVE 0.457831 0.866667
61 SRA 0.457831 0.855263
62 ATR 0.455556 0.902778
63 CA0 0.454545 0.831169
64 AU1 0.454545 0.855263
65 M33 0.454545 0.842105
66 2FD 0.45 0.802632
67 KG4 0.449438 0.831169
68 ACP 0.449438 0.88
69 50T 0.449438 0.866667
70 25A 0.447917 0.878378
71 7D7 0.445946 0.753425
72 ACQ 0.445652 0.88
73 T99 0.445652 0.844156
74 TAT 0.445652 0.844156
75 APR 0.444444 0.853333
76 AR6 0.444444 0.853333
77 A1R 0.443299 0.894737
78 A3R 0.443299 0.894737
79 ADP MG 0.443182 0.851351
80 ADP BEF 0.443182 0.851351
81 RAB 0.44 0.756757
82 ADN 0.44 0.756757
83 XYA 0.44 0.756757
84 AD9 0.43956 0.855263
85 AGS 0.43956 0.833333
86 ADV 0.43956 0.868421
87 RBY 0.43956 0.868421
88 CL9 0.4375 0.802632
89 AV2 0.43617 0.853333
90 NA7 0.434343 0.918919
91 6YZ 0.431579 0.88
92 ANP 0.430108 0.855263
93 ADS THS THS THS 0.42735 0.767442
94 A2R 0.427083 0.866667
95 HQG 0.427083 0.866667
96 SON 0.426966 0.893333
97 V2G 0.425532 0.858974
98 5AL 0.425532 0.842105
99 8LE 0.425532 0.810127
100 ANZ 0.424528 0.7875
101 APC MG 0.423913 0.853333
102 ADP PO3 0.423913 0.851351
103 ATP MG 0.423913 0.851351
104 QA7 0.42268 0.810127
105 GGZ 0.42268 0.768293
106 A22 0.42268 0.866667
107 3DH 0.421687 0.714286
108 TM1 0.421569 0.741176
109 ATF 0.421053 0.844156
110 ALF ADP 0.421053 0.7875
111 ANP MG 0.421053 0.842105
112 BEF ADP 0.419355 0.828947
113 5SV 0.418367 0.835443
114 ARJ 0.417722 0.712329
115 8LH 0.416667 0.820513
116 SRP 0.416667 0.868421
117 DGI 0.414894 0.883117
118 GAP 0.414894 0.807692
119 KL2 0.414634 0.824324
120 MTA 0.414634 0.714286
121 ADQ 0.414141 0.831169
122 4AD 0.414141 0.857143
123 ZZB 0.412281 0.761905
124 ACK 0.411765 0.847222
125 QQY 0.411765 0.802632
126 LMS 0.411765 0.75
127 FYA 0.411765 0.917808
128 PTJ 0.411765 0.8125
129 NB8 0.411765 0.835443
130 5N5 0.410256 0.733333
131 DLL 0.41 0.842105
132 MAP 0.408163 0.833333
133 8LQ 0.408163 0.844156
134 CC5 0.407895 0.777778
135 VO4 ADP 0.40625 0.855263
136 3UK 0.405941 0.831169
137 NWW 0.405063 0.69863
138 A4D 0.405063 0.733333
139 5CD 0.405063 0.743243
140 9ZA 0.40404 0.822785
141 8QN 0.40404 0.842105
142 9ZD 0.40404 0.822785
143 OOB 0.40404 0.842105
144 OZV 0.40404 0.853333
145 9SN 0.403846 0.790123
146 DTA 0.402439 0.75
147 A3G 0.402299 0.763158
148 NEC 0.402299 0.688312
149 2VA 0.402174 0.717949
150 5X8 0.402174 0.75
151 B5V 0.401961 0.820513
152 PR8 0.401961 0.860759
153 WAQ 0.401961 0.87013
154 AMO 0.4 0.868421
155 AFX 0.4 0.625
156 5AS 0.4 0.727273
157 PAJ 0.4 0.780488
158 QQX 0.4 0.792208
Similar Ligands (3D)
Ligand no: 1; Ligand: D5M; Similar ligands found: 146
No: Ligand Similarity coefficient
1 IMP 0.9716
2 TMP 0.9583
3 5GP 0.9581
4 UMP 0.9575
5 G 0.9554
6 UFP 0.9510
7 FMP 0.9494
8 BRU 0.9453
9 IRP 0.9451
10 6CG 0.9443
11 QBT 0.9441
12 NYM 0.9410
13 EO7 0.9409
14 XMP 0.9407
15 8OG 0.9404
16 C 0.9388
17 6MZ 0.9371
18 71V 0.9368
19 IMU 0.9360
20 C2R 0.9346
21 DCM 0.9339
22 5HU 0.9316
23 FDM 0.9312
24 AMZ 0.9308
25 U5P 0.9307
26 NIA 0.9299
27 8BR 0.9294
28 5IU 0.9294
29 8GM 0.9289
30 AOC 0.9284
31 DU 0.9275
32 ZAS 0.9251
33 BMP 0.9248
34 G7M 0.9240
35 8OP 0.9234
36 5FU 0.9232
37 UMC 0.9227
38 4X2 0.9227
39 U 0.9223
40 DUS 0.9219
41 C5P 0.9216
42 UP6 0.9213
43 PFU 0.9206
44 JLN 0.9203
45 N5O 0.9200
46 CMP 0.9200
47 BMQ 0.9197
48 H2U 0.9188
49 DC 0.9171
50 T3S 0.9165
51 Z8B 0.9158
52 A3N 0.9153
53 5BU 0.9152
54 2DT 0.9143
55 6SW 0.9135
56 MTM 0.9123
57 9L3 0.9120
58 TKW 0.9117
59 NUP 0.9107
60 D4M 0.9105
61 MTH 0.9100
62 5CM 0.9095
63 93A 0.9092
64 S5P 0.9071
65 FNU 0.9070
66 FN5 0.9066
67 DDN 0.9063
68 SSI 0.9058
69 5HM 0.9057
70 CAR 0.9057
71 NMN 0.9052
72 CNU 0.9048
73 PSU 0.9033
74 EP4 0.9028
75 MZP 0.9026
76 RVP 0.9024
77 RP1 0.8998
78 3Q0 0.8997
79 NWQ 0.8992
80 7CH 0.8968
81 FAI 0.8964
82 SP1 0.8964
83 16B 0.8955
84 ATM 0.8952
85 NCN 0.8951
86 DOC 0.8950
87 3Q1 0.8941
88 U4S 0.8936
89 U6M 0.8933
90 O7E 0.8925
91 6RE 0.8912
92 3F5 0.8908
93 DSH 0.8899
94 KB7 0.8899
95 2GE 0.8872
96 PCG 0.8871
97 J7C 0.8868
98 TXS 0.8862
99 6CN 0.8857
100 0RA 0.8837
101 460 0.8835
102 PWH 0.8834
103 3Q2 0.8832
104 MCF 0.8819
105 T3P 0.8813
106 U1S 0.8810
107 BVP 0.8809
108 MTE 0.8802
109 SU1 0.8798
110 35G 0.8798
111 U3S 0.8796
112 MT6 0.8794
113 FMC 0.8784
114 U2S 0.8774
115 GDP 0.8773
116 581 0.8769
117 8QB 0.8769
118 JFX 0.8731
119 HDU 0.8725
120 CH 0.8723
121 IXF 0.8704
122 9W8 0.8689
123 6SZ 0.8666
124 IYX 0.8657
125 9RK 0.8651
126 6U5 0.8647
127 JW5 0.8629
128 GNG 0.8628
129 75G 0.8616
130 GLY NIY 0.8614
131 SNP 0.8604
132 NWZ 0.8586
133 7PM 0.8584
134 6F3 0.8580
135 LIT 0.8579
136 100 0.8577
137 566 0.8572
138 GNH 0.8566
139 9ST 0.8562
140 873 0.8553
141 J90 0.8545
142 IMO 0.8537
143 HPR 0.8532
144 665 0.8532
145 PRH 0.8522
146 IMH 0.8505
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6LOZ; Ligand: ADE; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 6loz.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
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