Receptor
PDB id Resolution Class Description Source Keywords
5X8G 1.9 Å EC: 6.2.1.26 BINARY COMPLEX STRUCTURE OF A DOUBLE MUTANT I454RA456K OF O- SUCCINYLBENZOATE COA SYNTHETASE (MENE) FROM BACILLUS SUBTILW ITH ITS PRODUCT ANALOGUE OSB-NCOA AT 1.90 ANGSTROM BACILLUS SUBTILIS SUBSP. SUBTILIS STR.ORGANISM_TAXID: 224308 ADENYLATE-FORMING ENZYME ACYL-COA SYNTHETASE THIOESTER CONFORMATION COA PANTETHEINE TUNNEL ADP BINDING SUBSITEALTERNATION LARGE CONFORMATIONAL CHANGE INTER-DOMAIN LINKLIGASE
Ref.: CRYSTAL STRUCTURE OF THE THIOESTERIFICATION CONFORM BACILLUS SUBTILIS O-SUCCINYLBENZOYL-COA SYNTHETASE DISTINCT SUBSTRATE-BINDING MODE J. BIOL. CHEM. V. 292 12296 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
S0N C:508;
B:501;
D:501;
A:501;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
954.663 C32 H45 N8 O20 P3 CC(C)...
PEG D:507;
D:506;
A:510;
A:508;
A:509;
C:506;
C:507;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
106.12 C4 H10 O3 C(COC...
CA C:502;
C:503;
C:501;
A:505;
C:504;
B:505;
D:504;
A:506;
Invalid;
Part of Protein;
Part of Protein;
Part of Protein;
Invalid;
Invalid;
Invalid;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
MG A:502;
B:503;
A:504;
D:502;
B:504;
D:503;
B:502;
C:509;
A:503;
Part of Protein;
Part of Protein;
Invalid;
Part of Protein;
Invalid;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
NA A:507;
D:505;
C:505;
B:507;
B:506;
Invalid;
Part of Protein;
Invalid;
Invalid;
Part of Protein;
none;
none;
none;
none;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5X8G 1.9 Å EC: 6.2.1.26 BINARY COMPLEX STRUCTURE OF A DOUBLE MUTANT I454RA456K OF O- SUCCINYLBENZOATE COA SYNTHETASE (MENE) FROM BACILLUS SUBTILW ITH ITS PRODUCT ANALOGUE OSB-NCOA AT 1.90 ANGSTROM BACILLUS SUBTILIS SUBSP. SUBTILIS STR.ORGANISM_TAXID: 224308 ADENYLATE-FORMING ENZYME ACYL-COA SYNTHETASE THIOESTER CONFORMATION COA PANTETHEINE TUNNEL ADP BINDING SUBSITEALTERNATION LARGE CONFORMATIONAL CHANGE INTER-DOMAIN LINKLIGASE
Ref.: CRYSTAL STRUCTURE OF THE THIOESTERIFICATION CONFORM BACILLUS SUBTILIS O-SUCCINYLBENZOYL-COA SYNTHETASE DISTINCT SUBSTRATE-BINDING MODE J. BIOL. CHEM. V. 292 12296 2017
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5X8F - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 5X8G - S0N C32 H45 N8 O20 P3 CC(C)(CO[P....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5X8F - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 5X8G - S0N C32 H45 N8 O20 P3 CC(C)(CO[P....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5X8F - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 5X8G - S0N C32 H45 N8 O20 P3 CC(C)(CO[P....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: S0N; Similar ligands found: 127
No: Ligand ECFP6 Tc MDL keys Tc
1 S0N 1 1
2 SCO 0.816794 0.977012
3 0T1 0.78626 0.954545
4 DCA 0.784615 0.932584
5 COA 0.772727 0.954545
6 COW 0.771429 0.966292
7 CAO 0.768657 0.923077
8 CMX 0.762963 0.977012
9 ETB 0.757576 0.9
10 FCX 0.757353 0.944444
11 COS 0.755556 0.933333
12 30N 0.755556 0.875
13 AMX 0.755556 0.965517
14 2NE 0.75 0.955556
15 FAM 0.744526 0.933333
16 ACO 0.744526 0.923077
17 MCD 0.741007 0.955056
18 OXK 0.741007 0.955056
19 COK 0.741007 0.933333
20 SOP 0.741007 0.933333
21 SCA 0.739437 0.955056
22 HAX 0.73913 0.933333
23 BCO 0.737589 0.933333
24 CO6 0.735714 0.933333
25 CMC 0.735714 0.955056
26 BYC 0.734266 0.955056
27 2KQ 0.734266 0.934066
28 FYN 0.733813 0.954545
29 3KK 0.733813 0.933333
30 YE1 0.732394 0.965909
31 SCD 0.730496 0.977012
32 CA6 0.728571 0.848485
33 MLC 0.725352 0.955056
34 1HE 0.725352 0.913043
35 1VU 0.723404 0.923077
36 NMX 0.723404 0.884211
37 HGG 0.722222 0.955056
38 CA8 0.722222 0.867347
39 3CP 0.722222 0.955056
40 MCA 0.72028 0.944444
41 CAA 0.72028 0.94382
42 CAJ 0.71831 0.955056
43 2MC 0.71831 0.893617
44 FAQ 0.717241 0.955056
45 2CP 0.715278 0.944444
46 3HC 0.713287 0.94382
47 A1S 0.713287 0.933333
48 IVC 0.713287 0.94382
49 GRA 0.712329 0.955056
50 HXC 0.712329 0.913043
51 COF 0.710345 0.913043
52 0FQ 0.709459 0.955056
53 COO 0.708333 0.933333
54 BCA 0.705479 0.944444
55 MC4 0.703448 0.884211
56 CO8 0.702703 0.913043
57 HFQ 0.701987 0.955556
58 IRC 0.69863 0.94382
59 1GZ 0.69863 0.923077
60 5F9 0.697987 0.913043
61 MFK 0.697987 0.913043
62 ST9 0.697987 0.913043
63 DCC 0.697987 0.913043
64 UCC 0.697987 0.913043
65 MYA 0.697987 0.913043
66 TGC 0.695946 0.944444
67 HDC 0.695364 0.913043
68 4CA 0.693878 0.944444
69 1CZ 0.691275 0.944444
70 CIC 0.691275 0.955056
71 CS8 0.688742 0.903226
72 4CO 0.686667 0.944444
73 1HA 0.685897 0.955556
74 UOQ 0.684211 0.913043
75 NHW 0.684211 0.913043
76 NHM 0.684211 0.913043
77 0ET 0.682119 0.913043
78 01A 0.682119 0.913979
79 1CV 0.677632 0.955056
80 WCA 0.677632 0.934066
81 4KX 0.673203 0.923913
82 MRR 0.668831 0.913043
83 MRS 0.668831 0.913043
84 YNC 0.664516 0.923077
85 DAK 0.664516 0.923913
86 8Z2 0.660256 0.903226
87 COT 0.65625 0.955056
88 CA3 0.648148 0.955056
89 NHQ 0.641509 0.94382
90 01K 0.62963 0.933333
91 COD 0.628571 0.943182
92 CCQ 0.625806 0.893617
93 93P 0.625 0.966292
94 CA5 0.619048 0.913979
95 93M 0.606936 0.966292
96 UCA 0.605882 0.934066
97 CO7 0.597403 0.933333
98 OXT 0.562842 0.914894
99 JBT 0.550265 0.915789
100 4BN 0.548387 0.894737
101 5TW 0.548387 0.894737
102 BSJ 0.543478 0.945055
103 PLM COA 0.53012 0.88172
104 COA MYR 0.53012 0.88172
105 COA PLM 0.53012 0.88172
106 PAP 0.51938 0.793103
107 HMG 0.518072 0.922222
108 PPS 0.474074 0.71875
109 A3P 0.472868 0.781609
110 4YB 0.466216 0.755102
111 0WD 0.461538 0.791209
112 RFC 0.449438 0.934066
113 SFC 0.449438 0.934066
114 191 0.438596 0.848485
115 ACE SER ASP ALY THR NH2 COA 0.435644 0.912088
116 PTJ 0.421769 0.873563
117 A22 0.41958 0.816092
118 3AM 0.415385 0.770115
119 PUA 0.412121 0.822222
120 ATR 0.410072 0.781609
121 NA7 0.408163 0.83908
122 PAJ 0.40411 0.885057
123 A2D 0.402985 0.804598
124 A2R 0.402778 0.816092
125 3OD 0.402685 0.827586
126 SAP 0.4 0.769231
127 AGS 0.4 0.769231
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5X8G; Ligand: S0N; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5x8g.bio1) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5X8G; Ligand: S0N; Similar sites found: 119
This union binding pocket(no: 2) in the query (biounit: 5x8g.bio1) has 49 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3CV2 COA 0.01006 0.45855 1.4433
2 3A16 PXO 0.03318 0.40095 1.60858
3 5KOD AMP 0.0009797 0.48844 1.64948
4 4EPM AMP 0.003066 0.43777 1.64948
5 3TAO PGH 0.03408 0.41655 1.87266
6 4NOS ITU 0.04668 0.41267 1.87354
7 3H4L ANP 0.02728 0.40568 1.90736
8 1VPD TLA 0.04467 0.41698 2.00669
9 4XFR CIT 0.007723 0.46187 2.10773
10 4KBA 1QM 0.03476 0.40937 2.1148
11 4B2G V1N 0.001406 0.45626 2.26804
12 1CZA G6P 0.03509 0.41587 2.26804
13 4RDL FUC GAL NDG FUC 0.03434 0.42441 2.27273
14 3JQ3 ADP 0.03262 0.41758 2.45902
15 4YVN EBS 0.02935 0.43003 2.47423
16 2QLU ADE 0.0299 0.40768 2.54777
17 3T4L ZEA 0.008948 0.43236 2.59259
18 4LJ9 ACP 0.03077 0.41894 2.65487
19 1PQ7 ARG 0.03344 0.40713 2.67857
20 3Q3H UDP 0.03146 0.41843 2.68041
21 2D24 XYS XYS 0.02006 0.43247 2.75229
22 4K37 SAM 0.04041 0.40297 2.97297
23 5LE1 6UW 0.01138 0.45158 3.00752
24 3NZ1 3NY 0.01195 0.45132 3.06513
25 4KS7 X4Z 0.02374 0.40055 3.08219
26 4IRP UDP 0.04241 0.4206 3.18725
27 2H3H BGC 0.03932 0.4132 3.19489
28 3P2H NOO 0.01772 0.4178 3.48259
29 2GEK GDP 0.01027 0.44038 3.50515
30 1SW0 PGA 0.0428 0.40785 3.62903
31 3TW1 AHN 0.04967 0.41622 3.79747
32 3I9U DTU 0.03938 0.42444 3.91753
33 3RL3 5GP 0.04761 0.40228 4.05405
34 4NYT PC 0.002787 0.43624 4.14747
35 3A3B RBF 0.04349 0.41438 4.21053
36 2Z6J TUI 0.01104 0.4428 4.21687
37 2OUA AES 0.04147 0.42377 4.25532
38 2F6U CIT 0.02381 0.43298 4.2735
39 5F7J ADE 0.03201 0.42605 4.375
40 1O9W NAG 0.03207 0.424 4.51977
41 4WOE ADP 0.04131 0.4199 4.74227
42 3WV6 GAL BGC 0.0384 0.40833 4.74227
43 2BTM PGA 0.02757 0.42532 4.7619
44 5EYW PGA 0.02538 0.4273 4.81928
45 3IVV ASP GLU VAL THR SER THR THR SER SER SER 0.04409 0.41785 4.82759
46 1QKQ MAN 0.006357 0.44666 4.92958
47 4UWM FMN 0.04714 0.40562 5.02645
48 5M6N 7H9 0.04516 0.41905 5.08475
49 4RYV ZEA 0.04769 0.40865 5.16129
50 2NGR AF3 0.008838 0.45712 5.2356
51 5A7C 5D4 0.04734 0.40179 5.30973
52 5KJW 53C 0.04624 0.41588 5.36082
53 2G30 ALA ALA PHE 0.001614 0.42417 5.42636
54 2VDF OCT 0.005888 0.43198 5.5336
55 1XXR MAN 0.01969 0.43957 5.59006
56 1GT4 UNA 0.03661 0.40514 5.66038
57 5LUB 3Y7 0.01182 0.44875 5.72519
58 1I1E DM2 0.006732 0.46372 5.7732
59 1WPY BTN 0.008067 0.41119 5.95745
60 4SGA ACE PRO ALA PRO PHE 0.02019 0.42151 6.07735
61 1OJZ NAD 0.02269 0.41252 6.13208
62 5L83 ASP TRP GLU ILE VAL 0.03301 0.41381 6.25
63 5TCI MLI 0.02038 0.44172 6.34146
64 4DSU BZI 0.004155 0.47847 6.34921
65 4BG4 ADP 0.02428 0.41106 6.46067
66 1VBO MAN 0.02777 0.43038 6.71141
67 1F52 ADP 0.02176 0.42333 7.2165
68 5N58 93W 0.03593 0.41187 7.5188
69 1V59 NAD 0.02587 0.41939 7.74059
70 4YMZ 13P 0.03649 0.4186 7.96813
71 4DR9 BB2 0.02375 0.41789 8.33333
72 1V9A SAH 0.02694 0.41187 8.3682
73 5EY9 5SV 0.000006732 0.54595 8.65979
74 5HM3 649 0.000006052 0.52999 8.65979
75 2YPI PGA 0.03811 0.41393 9.31174
76 4ITH RCM 0.02467 0.405 10.2041
77 2XG5 EC2 0.03371 0.43154 10.4046
78 2XG5 EC5 0.03371 0.43154 10.4046
79 4TYT S3C 0.02952 0.42772 11.4537
80 5FUI APY 0.04081 0.41961 12.8788
81 5F6U 5VK 0.01508 0.44185 14.6497
82 1W6P NDG GAL 0.008277 0.46422 14.9254
83 5H2U 1N1 0.02775 0.4082 14.9813
84 3A1S GDP 0.04505 0.40667 15.5039
85 1PVC ILE SER GLU VAL 0.04163 0.40723 17.6471
86 2Y4O DLL 0.0000002395 0.43593 23.4763
87 2Y4N DLL 0.00002223 0.51114 24.4851
88 2Y4N PAC 0.0002029 0.49856 24.4851
89 5MST AMP 0.0000001218 0.66165 26.8041
90 5MST FUM 0.0000008609 0.58982 26.8041
91 4DG8 AMP 0.00004427 0.55062 27.6289
92 3KXW 1ZZ 0.000006454 0.54204 34.433
93 5MSD AMP 0.00000002335 0.71362 34.6392
94 5MSD BEZ 0.000000008854 0.70747 34.6392
95 2D1S SLU 0.0000001598 0.59354 35.8763
96 5OE4 3UK 0.0000005443 0.61692 36.6093
97 4R0M FA5 0.00000002505 0.466 37.732
98 3DHV DAL AMP 0.00000003677 0.6708 41.2371
99 4GR5 APC 0.00002952 0.56568 42.6804
100 4D57 ARG AMP 0.000000001884 0.6416 43.0928
101 4OXI GAP 0.00000004231 0.4384 43.5052
102 4GXQ ATP 0.0000002516 0.63235 43.7113
103 5N9X 8QN 0.00000001625 0.67948 43.9175
104 5N9X THR 0.000004748 0.64372 43.9175
105 5N9X ATP 0.0000003627 0.62504 43.9175
106 3NYQ AMP 0.000000000001032 0.77837 44.3564
107 3NYQ MCA 0.000000000002073 0.77433 44.3564
108 1MDB AMP DBH 0.000001659 0.60091 45.1546
109 3O84 HTJ 0.000006472 0.54669 45.9794
110 3C5E ATP 0.0000009949 0.48297 46.5979
111 1V25 ANP 0.0000002182 0.56893 47.0103
112 4RLQ 3SK 0.0000001537 0.54926 47.0103
113 3IES M24 0.0000006301 0.45943 47.2165
114 1PG4 PRX 0.00000001439 0.56829 48.0412
115 1PG4 COA 0.00000001439 0.56829 48.0412
116 5IE3 OXD 0.00000006991 0.45916 48.4536
117 5IE3 AMP 0.00000006991 0.45916 48.4536
118 3CW9 AMP 0.00000000346 0.74497 49.2784
119 3CW9 01A 0.000000003064 0.67559 49.2784
Pocket No.: 3; Query (leader) PDB : 5X8G; Ligand: S0N; Similar sites found: 33
This union binding pocket(no: 3) in the query (biounit: 5x8g.bio2) has 47 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1TV5 A26 0.03993 0.41135 1.58014
2 5X30 4LM 0.03754 0.4002 3.01508
3 1Y7P RIP 0.0429 0.41973 3.13901
4 1HPG BOC ALA ALA PRO GLU 0.02012 0.42356 3.20856
5 1BW9 PPY 0.04477 0.4022 3.37079
6 1GPM AMP 0.03469 0.40779 3.50515
7 3LGS ADE 0.01393 0.44587 3.74532
8 4G0P U5P 0.0436 0.42112 4.08163
9 3RGA LSB 0.03632 0.40382 4.24028
10 3CT5 NAG NAG NAG 0.04034 0.41855 4.40252
11 2PNC CLU 0.04837 0.41377 4.53608
12 4DO1 ANN 0.04019 0.41481 4.87805
13 3QH2 3NM 0.0441 0.41637 5.42986
14 5T46 MGP 0.03845 0.41881 6.06061
15 3TAY MN0 0.01352 0.40489 6.13497
16 1JPA ANP 0.0214 0.42502 6.41026
17 1WS1 BB2 0.04033 0.40153 6.41026
18 1U8Z GDP 0.01851 0.40391 6.54762
19 4DS0 A2G GAL NAG FUC 0.04692 0.42491 6.74847
20 1MRH FMC 0.04877 0.41389 7.01031
21 5E95 GDP 0.02505 0.40886 7.2165
22 5TQZ GLC 0.01841 0.43906 7.33333
23 1S17 GNR 0.02113 0.40949 8.88889
24 5TVA COA 0.04294 0.40015 9.16667
25 1DZK PRZ 0.04154 0.40088 11.465
26 2HYR BGC GLC 0.01491 0.42947 12.2951
27 2NU5 NAG 0.01403 0.42218 12.2951
28 2GUC MAN 0.01766 0.4118 12.2951
29 4OWK NGA 0.04 0.40272 12.3188
30 4UEC MGT 0.0336 0.42293 12.8205
31 5KWY C3S 0.01948 0.41739 14.17
32 3KMW ATP 0.03915 0.40218 32.5581
33 4FUT ATP 0.0000004363 0.40613 42.4742
Pocket No.: 4; Query (leader) PDB : 5X8G; Ligand: S0N; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5x8g.bio2) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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