Receptor
PDB id Resolution Class Description Source Keywords
1GIS 1.7 Å EC: 3.2.2.22 A TRICHOSANTHIN(TCS) MUTANT(E85Q) COMPLEX STRUCTURE WITH 2'- DEOXY-ADENOSIN-5'-MONOPHOSPHATE TRICHOSANTHES KIRILOWII PROTEIN-SUB COMPLEX TRICHOSANTHIN TCS HYDROLASE
Ref.: SUBSTRATE BINDING AND CATALYSIS IN TRICHOSANTHIN OCCUR IN DIFFERENT SITES AS REVEALED BY THE COMPLEX STRUCTURES OF SEVERAL E85 MUTANTS. PROTEIN ENG. V. 16 391 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DA A:438;
 Valid;
 none;
 submit data
331.222 C10 H14 N5 O6 P c1nc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1NLI 1.93 Å EC: 3.2.2.22 COMPLEX OF [E160A-E189A] TRICHOSANTHIN AND ADENINE TRICHOSANTHES KIRILOWII PROTEIN-DNA COMPLEX RIBOSOME-INACTIVATING PROTEIN HYDROLASE
Ref.: STRUCTURAL BASIS FOR THE INTERACTION OF [E160A-E189A]-TRICHOSANTHIN WITH ADENINE. TOXICON V. 41 575 2003
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 1GIU - ADE C5 H5 N5 c1[nH]c2c(....
2 1MRK - FMC C10 H13 N5 O4 c1nc2c(c(n....
3 1QD2 - ADE C5 H5 N5 c1[nH]c2c(....
4 1TCS - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
5 1MRJ - ADN C10 H13 N5 O4 c1nc(c2c(n....
6 1NLI Kd = 260 uM ADE C5 H5 N5 c1[nH]c2c(....
7 1GIS - DA C10 H14 N5 O6 P 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: DA; 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: DA; Similar ligands found: 97
No: Ligand Similarity coefficient
1 IMP 0.9634
2 TMP 0.9583
3 FMP 0.9577
4 UMP 0.9576
5 8OP 0.9562
6 5GP 0.9551
7 NYM 0.9518
8 G 0.9516
9 UFP 0.9510
10 9L3 0.9489
11 QBT 0.9476
12 IRP 0.9460
13 BRU 0.9453
14 8OG 0.9448
15 5CM 0.9409
16 6MZ 0.9405
17 5FU 0.9395
18 C2R 0.9394
19 C 0.9391
20 PFU 0.9381
21 71V 0.9370
22 8GM 0.9355
23 XMP 0.9353
24 EO7 0.9345
25 5IU 0.9342
26 FDM 0.9341
27 DCM 0.9338
28 5HU 0.9316
29 U5P 0.9307
30 FNU 0.9306
31 5BU 0.9299
32 G7M 0.9294
33 AMZ 0.9290
34 NIA 0.9284
35 DU 0.9275
36 AOC 0.9274
37 BMP 0.9248
38 UMC 0.9232
39 IMU 0.9231
40 A3N 0.9231
41 U 0.9223
42 DUS 0.9220
43 8BR 0.9216
44 C5P 0.9216
45 UP6 0.9213
46 ZAS 0.9205
47 N5O 0.9200
48 BMQ 0.9197
49 CNU 0.9187
50 H2U 0.9186
51 DC 0.9171
52 T3S 0.9163
53 NCN 0.9157
54 2DT 0.9143
55 TKW 0.9117
56 RVP 0.9108
57 NUP 0.9107
58 D4M 0.9105
59 4X2 0.9095
60 93A 0.9084
61 CH 0.9072
62 FN5 0.9072
63 S5P 0.9071
64 DDN 0.9064
65 CAR 0.9057
66 5HM 0.9057
67 PSU 0.9033
68 MZP 0.9027
69 NMN 0.9008
70 MTH 0.8986
71 16B 0.8984
72 U6M 0.8960
73 DOC 0.8953
74 ATM 0.8951
75 NWQ 0.8933
76 6RE 0.8912
77 JLN 0.8904
78 J7C 0.8895
79 EP4 0.8872
80 TXS 0.8862
81 BVP 0.8861
82 6CN 0.8857
83 FAI 0.8847
84 460 0.8833
85 KB7 0.8826
86 SNP 0.8803
87 FMC 0.8782
88 MCF 0.8753
89 MTE 0.8753
90 MTM 0.8657
91 CLM 0.8655
92 NOS 0.8647
93 IMH 0.8641
94 JFX 0.8606
95 AIR 0.8588
96 SNI 0.8560
97 BRX 0.8527
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1NLI; 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: 1nli.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
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