Receptor
PDB id Resolution Class Description Source Keywords
5TH5 2.41 Å EC: 4.3.99.3 CRYSTAL STRUCTURE OF QUEE FROM BACILLUS SUBTILIS WITH 6-CARB 5'-DEOXYADENOSYL ESTER BOUND BACILLUS SUBTILIS S-ADENOSYLMETHIONINE RADICAL ENZYME 7-CARBOXY-7-DEAZAGUANINSYNTHASE LYASE
Ref.: 7-CARBOXY-7-DEAZAGUANINE SYNTHASE: A RADICAL S-ADENOSYL-L-METHIONINE ENZYME WITH POLAR TENDENCIE J. AM. CHEM. SOC. V. 139 1912 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MET C:303;
D:303;
A:303;
B:303;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
149.211 C5 H11 N O2 S CSCC[...
7C5 A:302;
B:302;
C:302;
D:302;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
456.372 C17 H16 N10 O6 c1c(n...
SF4 B:301;
A:301;
D:301;
C:301;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
351.64 Fe4 S4 [S]12...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5TH5 2.41 Å EC: 4.3.99.3 CRYSTAL STRUCTURE OF QUEE FROM BACILLUS SUBTILIS WITH 6-CARB 5'-DEOXYADENOSYL ESTER BOUND BACILLUS SUBTILIS S-ADENOSYLMETHIONINE RADICAL ENZYME 7-CARBOXY-7-DEAZAGUANINSYNTHASE LYASE
Ref.: 7-CARBOXY-7-DEAZAGUANINE SYNTHASE: A RADICAL S-ADENOSYL-L-METHIONINE ENZYME WITH POLAR TENDENCIE J. AM. CHEM. SOC. V. 139 1912 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5TH5 - 7C5 C17 H16 N10 O6 c1c(nc2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5TH5 - 7C5 C17 H16 N10 O6 c1c(nc2c(n....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5TH5 - 7C5 C17 H16 N10 O6 c1c(nc2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MET; Similar ligands found: 32
No: Ligand ECFP6 Tc MDL keys Tc
1 MET 1 1
2 MED 1 1
3 DBB 0.518519 0.655172
4 ABA 0.518519 0.655172
5 2FM 0.514286 0.666667
6 NVA 0.5 0.758621
7 MF3 0.5 0.647059
8 DAB 0.466667 0.636364
9 HSE 0.466667 0.617647
10 SME 0.457143 0.717949
11 MHO 0.457143 0.717949
12 HCS 0.451613 0.733333
13 API 0.451613 0.606061
14 CDT 0.447368 0.756757
15 2MM 0.444444 0.657143
16 NLE 0.441176 0.766667
17 ONL 0.441176 0.71875
18 UN1 0.428571 0.606061
19 11C 0.428571 0.606061
20 MSE 0.428571 0.9
21 GGL 0.424242 0.625
22 GLU 0.424242 0.625
23 DGL 0.424242 0.625
24 CBH 0.418605 0.685714
25 ORN 0.411765 0.65625
26 AME 0.410256 0.771429
27 FME 0.410256 0.84375
28 LEU 0.40625 0.666667
29 CYS 0.4 0.666667
30 C2N 0.4 0.633333
31 DCY 0.4 0.666667
32 JM6 0.4 0.7
Ligand no: 2; Ligand: 7C5; Similar ligands found: 166
No: Ligand ECFP6 Tc MDL keys Tc
1 7C5 1 1
2 SON 0.55 0.833333
3 AOC 0.515152 0.821918
4 AMP 0.494949 0.815789
5 A 0.494949 0.815789
6 AD9 0.485981 0.797468
7 CA0 0.485714 0.820513
8 AMP MG 0.485149 0.772152
9 G5A 0.481481 0.7
10 ABM 0.480392 0.772152
11 A2D 0.480392 0.818182
12 LEU LMS 0.478261 0.684783
13 SRA 0.475248 0.775
14 5AL 0.472727 0.831169
15 ADX 0.471698 0.72093
16 AU1 0.471698 0.797468
17 M33 0.471698 0.78481
18 A12 0.471154 0.7875
19 AP2 0.471154 0.7875
20 BA3 0.471154 0.818182
21 TSB 0.469027 0.715909
22 A5A 0.468468 0.724138
23 B4P 0.466667 0.818182
24 ADP 0.466667 0.818182
25 AP5 0.466667 0.818182
26 5AS 0.466667 0.681319
27 SSA 0.464286 0.7
28 GAP 0.463636 0.820513
29 5CD 0.463158 0.805556
30 APR 0.462963 0.818182
31 AR6 0.462963 0.818182
32 RAB 0.462366 0.819444
33 ADN 0.462366 0.819444
34 XYA 0.462366 0.819444
35 AN2 0.462264 0.807692
36 NSS 0.46087 0.7
37 54H 0.460177 0.707865
38 52H 0.460177 0.7
39 VMS 0.460177 0.707865
40 G3A 0.459016 0.896104
41 SAP 0.458716 0.777778
42 RBY 0.458716 0.7875
43 AGS 0.458716 0.777778
44 ADV 0.458716 0.7875
45 ADP MG 0.457944 0.78481
46 1ZZ 0.457627 0.752941
47 00A 0.456897 0.8125
48 53H 0.45614 0.7
49 5CA 0.45614 0.7
50 G5P 0.455285 0.896104
51 MYR AMP 0.453782 0.752941
52 50T 0.453704 0.78481
53 ATP 0.453704 0.818182
54 ADP BEF 0.453704 0.765432
55 BEF ADP 0.453704 0.765432
56 ACP 0.453704 0.797468
57 5N5 0.452632 0.794521
58 OOB 0.452174 0.855263
59 GTA 0.451613 0.8625
60 SRP 0.451327 0.810127
61 ANP 0.45045 0.797468
62 ACQ 0.45045 0.797468
63 5FA 0.449541 0.818182
64 PRX 0.449541 0.753086
65 AQP 0.449541 0.818182
66 APC 0.449541 0.7875
67 GSU 0.449153 0.719101
68 P5A 0.449153 0.670213
69 WAQ 0.449153 0.790123
70 DSZ 0.448276 0.719101
71 PAJ 0.448276 0.771084
72 LSS 0.448276 0.684783
73 A4D 0.447917 0.794521
74 ADP PO3 0.445455 0.815789
75 NVA LMS 0.444444 0.684783
76 DTA 0.444444 0.786667
77 MAP 0.443478 0.777778
78 DAL AMP 0.443478 0.831169
79 ATF 0.442478 0.7875
80 A4P 0.44186 0.8
81 ATP MG 0.441441 0.78481
82 3UK 0.440678 0.868421
83 SFG 0.440367 0.797297
84 5SV 0.439655 0.717647
85 8QN 0.439655 0.831169
86 TAT 0.4375 0.7875
87 PR8 0.436975 0.761905
88 KAA 0.436975 0.677419
89 ZAS 0.436893 0.766234
90 AMO 0.435897 0.810127
91 4AD 0.435897 0.8
92 EP4 0.434343 0.753247
93 NB8 0.433333 0.780488
94 TXA 0.433333 0.810127
95 SA8 0.432432 0.75
96 AHX 0.432203 0.759036
97 DLL 0.432203 0.855263
98 3DH 0.431373 0.773333
99 YSA 0.430894 0.719101
100 M2T 0.43 0.734177
101 MAO 0.429907 0.697674
102 ADP ALF 0.429825 0.756098
103 ALF ADP 0.429825 0.756098
104 OAD 0.428571 0.820513
105 SAI 0.428571 0.779221
106 4UV 0.427419 0.822785
107 5X8 0.427273 0.810811
108 WSA 0.426357 0.727273
109 OMR 0.426357 0.744186
110 649 0.426357 0.688172
111 9SN 0.42623 0.825
112 ANP MG 0.426087 0.756098
113 VO4 ADP 0.426087 0.78481
114 ADP VO4 0.426087 0.78481
115 MTA 0.425743 0.773333
116 LAQ 0.425197 0.752941
117 LAD 0.425 0.771084
118 A1R 0.423729 0.746988
119 ADQ 0.423729 0.820513
120 YAP 0.422764 0.822785
121 LPA AMP 0.421875 0.752941
122 ME8 0.421488 0.752941
123 PTJ 0.421488 0.802469
124 3OD 0.421488 0.820513
125 BIS 0.421488 0.768293
126 EEM 0.421053 0.731707
127 4UU 0.420635 0.822785
128 GJV 0.420561 0.818182
129 TYR AMP 0.419355 0.833333
130 6RE 0.419048 0.828947
131 A22 0.418803 0.831169
132 TAD 0.417323 0.75
133 ADP BMA 0.416667 0.820513
134 25A 0.415254 0.842105
135 A3G 0.415094 0.8
136 G A A A 0.414815 0.896104
137 AHZ 0.414062 0.77381
138 4TC 0.412214 0.780488
139 FA5 0.41129 0.833333
140 A3N 0.411215 0.763158
141 J7C 0.411215 0.84
142 7MD 0.409449 0.752941
143 AAT 0.408696 0.707317
144 XAH 0.408 0.732558
145 UP5 0.407692 0.8
146 4UW 0.407692 0.792683
147 NAI 0.407692 0.790123
148 S4M 0.407407 0.666667
149 4YB 0.40625 0.741573
150 MHZ 0.405405 0.659091
151 AMP DBH 0.404762 0.820513
152 TYM 0.40458 0.833333
153 SAH 0.403509 0.789474
154 GEK 0.403361 0.782051
155 DSH 0.401869 0.725
156 NEC 0.401869 0.746667
157 S7M 0.401709 0.731707
158 SMM 0.401709 0.72619
159 A A 0.401639 0.818182
160 UPA 0.401515 0.790123
161 DZD 0.40146 0.771084
162 BT5 0.40146 0.747126
163 U A G G 0.40146 0.907895
164 48N 0.4 0.825
165 3AM 0.4 0.779221
166 SAM 0.4 0.731707
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5TH5; Ligand: 7C5; Similar sites found: 9
This union binding pocket(no: 1) in the query (biounit: 5th5.bio2) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4JYD SAH 0.004434 0.40749 5.70342
2 5VSM 5AD 0.0007896 0.41611 7.22433
3 5VSM MET 0.0009058 0.4137 7.22433
4 4FHD EEM 0.006339 0.40373 8.74525
5 4FHD 0TT 0.006339 0.40373 8.74525
6 2FB3 GTP 0.001655 0.42499 12.1673
7 4K39 SAM 0.0006346 0.40893 17.1103
8 4K38 SAM 0.000995 0.40644 17.1103
9 4K37 SAM 0.0006823 0.40194 17.1103
Pocket No.: 2; Query (leader) PDB : 5TH5; Ligand: 7C5; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5th5.bio2) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5TH5; Ligand: MET; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5th5.bio2) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5TH5; Ligand: MET; Similar sites found: 80
This union binding pocket(no: 4) in the query (biounit: 5th5.bio2) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4HXY NDP 0.008479 0.44124 0.913242
2 2IVD FAD 0.01878 0.4302 1.90114
3 3G6K FAD 0.02791 0.41463 2.28137
4 3G6K POP 0.0253 0.41463 2.28137
5 4XVX P6G FDA 0.01488 0.43049 2.6616
6 4XVX P33 FDA 0.01736 0.42797 2.6616
7 2I0D MUT 0.04024 0.42792 3.0303
8 4RJK TPP 0.01477 0.42458 3.04183
9 2GU8 796 0.04488 0.41951 3.04183
10 4PAB THG 0.01713 0.40712 3.04183
11 4K26 NDP 0.04371 0.40295 3.04183
12 3LXN MI1 0.02446 0.40274 3.04183
13 4ITH RCM 0.02588 0.40148 3.04183
14 3NUG NAD 0.03325 0.40939 3.23887
15 4O0L NDP 0.02362 0.41741 3.42205
16 1Q19 APC 0.01539 0.4148 3.42205
17 5JZJ AN2 0.0185 0.40348 3.42205
18 2DFV NAD 0.03523 0.40322 3.42205
19 4Q5M ROC 0.0199 0.4214 3.44828
20 2A9D MTE 0.008548 0.42622 3.80228
21 1CZI PRO PHI SMC NOR 0.01018 0.42574 3.80228
22 1SOX MTE 0.009113 0.42479 3.80228
23 4XQC NAD 0.04609 0.41295 3.80228
24 3EPO MP5 0.01761 0.40834 3.80228
25 1WPQ NAD 0.02519 0.4068 3.80228
26 2ZL4 ALA ALA ALA ALA 0.0123 0.40063 4.08163
27 5ULJ 0WD 0.009756 0.42502 4.18251
28 4L2I NAD 0.04564 0.41398 4.18251
29 1PJ6 FOL 0.01612 0.41208 4.56274
30 3QXV MTX 0.008087 0.42366 4.7619
31 4F9C 0SX 0.01478 0.40842 4.86111
32 2E5A LAQ 0.0232 0.41417 4.94297
33 3TAY MN0 0.02116 0.41222 5.52147
34 5EW9 5VC 0.01284 0.4715 5.53506
35 4I54 1C1 0.03726 0.40557 5.70342
36 2GZ3 NAP 0.03368 0.42449 6.08365
37 3AAQ ARU 0.04064 0.40985 6.08365
38 1WA5 GTP 0.04516 0.40105 6.25
39 4EWN 0VR 0.008927 0.41947 6.32411
40 5BVE 4VG 0.01495 0.45011 6.46388
41 1ERB ETR 0.0352 0.40324 7.10383
42 1D1G NDP 0.02522 0.40821 7.14286
43 5VSM MET 0.00000005934 0.68952 7.22433
44 5VSM 5AD 0.0000002836 0.65486 7.22433
45 1IIU RTL 0.02026 0.40863 7.47126
46 4EUU BX7 0.03698 0.40079 7.60456
47 3MJE NDP 0.02736 0.4128 7.98479
48 2PD4 DCN 0.0401 0.40919 7.98479
49 2PD4 NAD 0.04044 0.40899 7.98479
50 5GZ9 ANP 0.02846 0.40252 7.98479
51 2B4Q NAP 0.04397 0.40168 7.98479
52 4J1Q NDP 0.02087 0.41662 8.36502
53 4XIZ LPP 0.01339 0.43182 8.57143
54 5WGG SAM 0.000009687 0.56832 8.74525
55 4FHD EEM 0.002517 0.46936 8.74525
56 4FHD 0TT 0.002517 0.46936 8.74525
57 5C5H 4YB 0.01057 0.43092 8.74525
58 2BKK ADP 0.0117 0.41354 8.87574
59 3GGO ENO 0.04753 0.41056 9.5057
60 3GGO NAI 0.04753 0.41056 9.5057
61 3A7R LAQ 0.01124 0.43929 9.88593
62 2DC1 NAD 0.01981 0.41782 10.5932
63 4R38 RBF 0.02262 0.4045 10.7143
64 4PIV NDP 0.03296 0.40959 11.4068
65 2FB3 GTP 0.00006312 0.55117 12.1673
66 2FB3 5AD 0.00001983 0.54974 12.1673
67 2FB3 MET 0.00001715 0.54974 12.1673
68 3RFA SAM 0.006948 0.427 12.1673
69 1MJH ATP 0.02283 0.40594 12.963
70 1KOJ PAN 0.02487 0.40237 13.308
71 5CLO NS8 0.000596 0.44056 15.2542
72 3O9L LPN 0.04328 0.4111 16.8675
73 4K38 SAM 0.000006838 0.58166 17.1103
74 4K37 SAM 0.00001913 0.55349 17.1103
75 4K39 SAM 0.0000263 0.54933 17.1103
76 5THQ NDP 0.0446 0.40135 18.3824
77 1OLT SAM 0.002188 0.45449 22.0532
78 4M7T SAM 0.00003648 0.54216 22.4335
79 2JBM SRT 0.008558 0.41261 24.4147
80 3C8F MT2 0.0003852 0.42268 31.8367
Pocket No.: 5; Query (leader) PDB : 5TH5; Ligand: MET; Similar sites found: 55
This union binding pocket(no: 5) in the query (biounit: 5th5.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1PQ7 ARG 0.02141 0.40281 1.78571
2 1WUB OTP 0.04114 0.41584 1.90114
3 2ZB3 NDP 0.03331 0.40905 1.90114
4 2WK9 PLG 0.04192 0.40459 1.90114
5 2JLD AG1 0.04699 0.4027 1.90114
6 1EQ2 NAP 0.04391 0.40229 1.90114
7 2WK9 PLP 0.04874 0.40011 1.90114
8 5EOB 5QQ 0.04609 0.41851 2.28137
9 3AB1 FAD 0.04489 0.41113 2.28137
10 4FBL SPD 0.009301 0.41084 2.28137
11 1FK8 NAD 0.03238 0.40551 2.33463
12 4ZFL 4NK 0.02328 0.40928 2.5641
13 2XMY CDK 0.01815 0.44834 2.6616
14 1CT9 GLN 0.01202 0.40785 2.6616
15 1E6E FAD 0.04831 0.40732 2.6616
16 5LI1 ANP 0.03053 0.40028 2.6616
17 3HGM ATP 0.009688 0.42624 2.72109
18 3B2Q ATP 0.01054 0.42792 3.04183
19 1DNP FAD 0.03534 0.40479 3.04183
20 4UCI SAM 0.02549 0.40391 3.04183
21 4WB6 ATP 0.03601 0.40213 3.04183
22 1UPA TPP 0.03651 0.40169 3.04183
23 4U63 FAD 0.02924 0.40982 3.42205
24 4O8A FAD 0.04898 0.40173 3.42205
25 2JAJ D20 0.0247 0.4001 3.42205
26 1JJE BYS 0.01974 0.40967 3.6036
27 1VEM GLC GLC 0.04048 0.40437 3.80228
28 2RKV COA 0.04901 0.40296 3.80228
29 3HQP FDP 0.01726 0.40047 3.80228
30 1HDO NAP 0.0389 0.40927 3.8835
31 4L2I FAD 0.04153 0.40927 4.18251
32 2PI8 NAG NAG NAG NAG NAG NAG 0.04987 0.4017 4.18251
33 3AFN NAP 0.04918 0.40309 4.26357
34 2V3A FAD 0.0334 0.41687 4.56274
35 1RSG FAD 0.03938 0.41516 4.56274
36 4I53 1C1 0.02747 0.40159 4.56274
37 3A4T SFG 0.03193 0.40375 5.70342
38 4Z3E GAL NGA GLA BGC GAL 0.006582 0.40369 6.06061
39 1J49 NAD 0.04229 0.40418 6.08365
40 2IHU TP9 0.04659 0.40612 6.46388
41 4X1T UDP 0.02145 0.40224 6.46388
42 1O94 AMP 0.02149 0.40531 6.84411
43 2CUL FAD 0.02923 0.41822 7.60456
44 1FHX 4IP 0.01572 0.40185 7.75194
45 1M5W DXP 0.03715 0.40944 7.81893
46 3M2W L8I 0.01262 0.4097 7.98479
47 4BHN BH9 0.02212 0.40562 7.98479
48 3WXB NDP 0.04688 0.4022 8.36502
49 1Y8Q ATP 0.03402 0.40349 9.5057
50 5LDQ NAP 0.02032 0.40057 9.60452
51 4J75 TYM 0.04175 0.40059 10.6464
52 5U98 1KX 0.0482 0.41072 12.1212
53 5LFV SIA GAL NAG 0.009294 0.41314 13.308
54 5EB4 FAD 0.04119 0.4154 16.73
55 4WNK 453 0.03151 0.40936 20.9125
Pocket No.: 6; Query (leader) PDB : 5TH5; Ligand: MET; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5th5.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5TH5; Ligand: 7C5; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 5th5.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 5TH5; Ligand: 7C5; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 5th5.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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