Receptor
PDB id Resolution Class Description Source Keywords
3EXS 2.5 Å EC: 4.1.1.85 CRYSTAL STRUCTURE OF KGPDC FROM STREPTOCOCCUS MUTANS IN COMPLEX WITH D-R5P STREPTOCOCCUS MUTANS BETA BARREL LYASE
Ref.: OPEN-CLOSED CONFORMATIONAL CHANGE REVEALED BY THE CRYSTAL STRUCTURES OF 3-KETO-L-GULONATE 6-PHOSPHATE DECARBOXYLASE FROM STREPTOCOCCUS MUTANS BIOCHEM.BIOPHYS.RES.COMMUN. V. 381 429 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5RP A:501;
D:502;
Valid;
Valid;
none;
none;
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230.11 C5 H11 O8 P C([C@...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3EXS 2.5 Å EC: 4.1.1.85 CRYSTAL STRUCTURE OF KGPDC FROM STREPTOCOCCUS MUTANS IN COMPLEX WITH D-R5P STREPTOCOCCUS MUTANS BETA BARREL LYASE
Ref.: OPEN-CLOSED CONFORMATIONAL CHANGE REVEALED BY THE CRYSTAL STRUCTURES OF 3-KETO-L-GULONATE 6-PHOSPHATE DECARBOXYLASE FROM STREPTOCOCCUS MUTANS BIOCHEM.BIOPHYS.RES.COMMUN. V. 381 429 2009
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3EXS - 5RP C5 H11 O8 P C([C@H]([C....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3EXS - 5RP C5 H11 O8 P C([C@H]([C....
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1SO6 - TX4 C4 H12 N O8 P C([C@@H]([....
2 1Q6R - LX1 C5 H13 O7 P C[C@H]([C@....
3 1KW1 - LG6 C6 H13 O10 P C([C@@H]([....
4 1SO4 - TX4 C4 H12 N O8 P C([C@@H]([....
5 1XBV - 5RP C5 H11 O8 P C([C@H]([C....
6 1Q6Q - LXP C5 H13 O8 P C([C@H]([C....
7 1SO5 - TX4 C4 H12 N O8 P C([C@@H]([....
8 1Q6L - TX4 C4 H12 N O8 P C([C@@H]([....
9 1SO3 - TX4 C4 H12 N O8 P C([C@@H]([....
10 1Q6O - LG6 C6 H13 O10 P C([C@@H]([....
11 1XBX - HMS C5 H11 O8 P C([C@@H]([....
12 1XBZ - LX1 C5 H13 O7 P C[C@H]([C@....
13 1XBY - 5RP C5 H11 O8 P C([C@H]([C....
14 3EXS - 5RP C5 H11 O8 P C([C@H]([C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5RP; Similar ligands found: 45
No: Ligand ECFP6 Tc MDL keys Tc
1 5RP 1 1
2 HMS 1 1
3 5SP 1 1
4 RUB 0.657895 0.944444
5 XBP 0.657895 0.944444
6 TG6 0.641026 0.972222
7 F6R 0.641026 0.972222
8 I22 0.609756 0.972222
9 DER 0.594595 0.891892
10 DEZ 0.594595 0.891892
11 DXP 0.578947 0.815789
12 RES 0.536585 0.673469
13 PA5 0.512195 0.891892
14 R10 0.512195 0.891892
15 P6F 0.5 0.944444
16 M2P 0.5 0.916667
17 P6T 0.5 0.944444
18 2FP 0.5 0.944444
19 LG6 0.488372 0.891892
20 6PG 0.488372 0.891892
21 HG3 0.485714 0.783784
22 PAN 0.466667 0.673469
23 4TP 0.452381 0.75
24 LXP 0.45 0.944444
25 A5P 0.45 0.944444
26 DX5 0.45 0.944444
27 LX1 0.45 0.815789
28 RBL 0.444444 0.638889
29 QDK 0.444444 0.638889
30 XUL 0.444444 0.638889
31 S6P 0.439024 0.916667
32 KD0 0.425532 0.891892
33 E4P 0.425 0.861111
34 5FX 0.421053 0.605263
35 DG6 0.418605 0.918919
36 TX4 0.418605 0.632653
37 R5P 0.418605 0.916667
38 R52 0.418605 0.916667
39 3PG 0.410256 0.837838
40 H4P 0.408163 0.772727
41 52L 0.408163 0.723404
42 DG2 0.404762 0.810811
43 AGP 0.4 0.75
44 G6Q 0.4 0.916667
45 M6R 0.4 0.75
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3EXS; Ligand: 5RP; Similar sites found: 210
This union binding pocket(no: 1) in the query (biounit: 3exs.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3QMN COA 0.01044 0.41278 None
2 5HCY 60D 0.03962 0.40751 0.904977
3 4P5E N6P 0.01465 0.40197 1.31579
4 4MN7 SME 0.007408 0.40731 1.34228
5 4JIQ 1L5 0.0008048 0.47612 1.35747
6 4JIQ FMN 0.0008048 0.47612 1.35747
7 4D57 ARG AMP 0.01283 0.42742 1.35747
8 2XVD AS6 0.01375 0.41757 1.80995
9 1OVD FMN 0.000369 0.50788 2.26244
10 1OVD ORO 0.000369 0.50788 2.26244
11 3W9Z FMN 0.0001471 0.50025 2.26244
12 1GTE FMN 0.0007314 0.49006 2.26244
13 1GTE IUR 0.0007314 0.49006 2.26244
14 2RJH DCS 0.002517 0.43423 2.26244
15 1ZQ5 NAP 0.04138 0.41545 2.26244
16 1ZQ5 E04 0.04138 0.41545 2.26244
17 3NTY 5P3 0.02818 0.41448 2.26244
18 3NTY NAP 0.02836 0.41343 2.26244
19 3C5E ATP 0.04761 0.41078 2.26244
20 2Z6I FMN 0.0002392 0.40894 2.26244
21 3AAQ ARU 0.03729 0.40436 2.26244
22 2Q3O FMN 0.00001784 0.55173 2.71493
23 4EWN 0VR 0.0000316 0.52706 2.71493
24 1UUO FMN 0.0005088 0.51748 2.71493
25 1UUO BRF 0.0005479 0.51748 2.71493
26 1UUO ORO 0.0005088 0.51748 2.71493
27 4QNW FMN 0.0002288 0.49543 2.71493
28 1BWV CAP 0.0005378 0.47312 2.71493
29 2GOU FMN 0.002944 0.45789 2.71493
30 4M5P FMN 0.003091 0.44034 2.71493
31 1NJJ ORX 0.003402 0.43831 2.71493
32 2BLE 5GP 0.00696 0.43243 2.71493
33 2C6Q NDP 0.01427 0.43184 2.71493
34 2C6Q IMP 0.00608 0.43096 2.71493
35 1UJP CIT 0.0006971 0.42507 2.71493
36 5VSM 5AD 0.00666 0.42228 2.71493
37 5VSM MET 0.006889 0.42157 2.71493
38 1ICP FMN 0.00007756 0.53196 3.16742
39 2Y88 2ER 0.0001632 0.52475 3.16742
40 4NAE 1GP 0.0001153 0.51371 3.16742
41 4WZH FMN 0.0005144 0.48577 3.16742
42 2F6U CIT 0.0003121 0.48441 3.16742
43 4XP7 FNR 0.0005256 0.4736 3.16742
44 1OYB HBA 0.002755 0.45113 3.16742
45 1OYB FMN 0.0022 0.45113 3.16742
46 4TMC FMN 0.002092 0.45044 3.16742
47 4TMC HBA 0.002713 0.44831 3.16742
48 3OIX FMN 0.002795 0.44601 3.16742
49 4I2D APC 0.01285 0.41175 3.16742
50 3CV6 NAP 0.03248 0.40941 3.16742
51 3CV6 HXS 0.03381 0.40941 3.16742
52 1VJY 460 0.03164 0.40283 3.16742
53 1FDJ 2FP 0.01061 0.40237 3.16742
54 3B0P FMN 0.000002093 0.58318 3.61991
55 2HSA FMN 0.00006471 0.53591 3.61991
56 2YPI PGA 0.0000524 0.50761 3.61991
57 1Z48 FMN 0.0001694 0.49235 3.61991
58 1Z41 FMN 0.0001784 0.49128 3.61991
59 1PS9 FMN 0.0003445 0.4888 3.61991
60 3ATY FMN 0.001374 0.46292 3.61991
61 4CW5 FMN 0.0008993 0.46236 3.61991
62 5OCS FMN 0.0009345 0.46156 3.61991
63 1Z44 FMN 0.0002005 0.45795 3.61991
64 3C3N FMN 0.006519 0.44257 3.61991
65 1Z42 FMN 0.001143 0.4368 3.61991
66 2B4G FMN 0.005557 0.43591 3.61991
67 2HQM FAD 0.04074 0.4077 3.61991
68 1VKF CIT 0.0006275 0.4226 3.7234
69 1PVN MZP 0.001907 0.47456 4.0724
70 1AL8 DHP 0.001301 0.47188 4.0724
71 1AL8 FMN 0.0009559 0.46894 4.0724
72 1ME8 RVP 0.002823 0.46241 4.0724
73 1JCM 137 0.0008862 0.46046 4.0724
74 1P4C FMN 0.005638 0.44102 4.0724
75 5FI4 5XV 0.008677 0.42175 4.0724
76 4WAS NAP 0.03058 0.40887 4.0724
77 1CSI OAA 0.03561 0.40822 4.0724
78 5L9O GOP 0.01691 0.40426 4.0724
79 3O84 HTJ 0.02349 0.40317 4.0724
80 2F69 SAH 0.01027 0.40304 4.0724
81 5EYW PGA 0.00008244 0.48816 4.52489
82 1OFD AKG 0.0008596 0.48516 4.52489
83 1OFD FMN 0.0009764 0.48491 4.52489
84 3MJY IJZ 0.0008211 0.48481 4.52489
85 3MJY FMN 0.0008211 0.48481 4.52489
86 4I9A NCN 0.0008192 0.4621 4.52489
87 1TUF AZ1 0.003815 0.44099 4.52489
88 2B6N ALA PRO THR 0.004996 0.43281 4.52489
89 4LUT DCS 0.004204 0.42804 4.52489
90 4K38 SAM 0.01313 0.40613 4.52489
91 4K39 SAM 0.01456 0.4021 4.52489
92 3PDT ADP 0.01319 0.40011 4.52489
93 4HKP TKW 0.00004514 0.532 4.80769
94 4HKP 16B 0.00003646 0.52943 4.80769
95 3VKC FPQ 0.00004666 0.52906 4.97738
96 3TAO PGH 0.00006917 0.50199 4.97738
97 2BTM PGA 0.0000935 0.48639 4.97738
98 5CSS G3P 0.0009531 0.4427 4.97738
99 1VHN FMN 0.00502 0.41769 4.97738
100 2C91 NAP 0.03759 0.40219 4.97738
101 3IS2 FAD 0.02916 0.40106 5.19481
102 4OHB 5HM 0.009207 0.40289 5.26316
103 4UTW RFW 0.000006623 0.55936 5.42986
104 4UTU LRY 0.000007437 0.55387 5.42986
105 3KRU FMN 0.00005342 0.54508 5.42986
106 1DBT U5P 0.00003113 0.53274 5.42986
107 1DQX BMP 0.00004978 0.52769 5.42986
108 2OEM 1AE 0.00005496 0.50981 5.42986
109 1VYP TNF 0.0003309 0.49348 5.42986
110 1VYP FMN 0.0003598 0.49348 5.42986
111 3HF3 FMN 0.0006163 0.47644 5.42986
112 4YNU LGC 0.03945 0.41312 5.42986
113 4YNU FAD 0.03836 0.41073 5.42986
114 2VJJ RAM GLC GAL NAG NAG GLC 0.03079 0.40456 5.42986
115 4BFM ANP 0.01692 0.40255 5.42986
116 2PLK P3D 0.001292 0.45881 5.48926
117 1SW0 PGA 0.00003168 0.52105 5.88235
118 5GJO PLP 0.0008577 0.45636 5.88235
119 4AF0 IMP 0.002182 0.44954 5.88235
120 2NVA PL2 0.004717 0.43797 5.88235
121 4JEM C5P 0.00642 0.42306 5.88235
122 5DEY 59T 0.04249 0.41209 5.88235
123 4WHZ 3NL 0.04402 0.4083 5.88235
124 4UWH JXM 0.003563 0.40595 5.88235
125 3LF0 ATP 0.01708 0.40565 6.14035
126 3KDN CAP 0.00005957 0.56107 6.33484
127 3MI2 PFU 0.0001372 0.54299 6.33484
128 2QCD U5P 0.00002891 0.53679 6.33484
129 2Q8Z NUP 0.0001063 0.51587 6.33484
130 4IGH FMN 0.001352 0.50169 6.33484
131 4IGH ORO 0.001352 0.50169 6.33484
132 4IGH 1EA 0.001352 0.50169 6.33484
133 1WDD CAP 0.0005652 0.47424 6.33484
134 2RDT FMN 0.000904 0.47362 6.33484
135 2RDT 2RD 0.001282 0.47362 6.33484
136 3AXK NDP 0.0004322 0.47298 6.33484
137 1KBI PYR 0.001222 0.46873 6.33484
138 1KBJ FMN 0.001797 0.45881 6.33484
139 4N02 FNR 0.003516 0.44274 6.33484
140 2E7Z MGD 0.02382 0.41352 6.33484
141 1NAA ABL 0.04679 0.41187 6.33484
142 1NAA 6FA 0.0392 0.40942 6.33484
143 1IR1 CAP 0.0003378 0.48507 6.50407
144 1RBO CAP 0.008613 0.48018 6.50407
145 3OVR 5SP 0.000004678 0.58019 6.78733
146 4A3U FMN 0.001351 0.45787 6.78733
147 3LXN MI1 0.01697 0.40249 6.78733
148 4R38 RBF 0.01744 0.40192 7.14286
149 1QDS PGA 0.00003637 0.515 7.23982
150 4ORM 2V6 0.001065 0.50661 7.23982
151 4ORM FMN 0.001065 0.50661 7.23982
152 4ORM ORO 0.001065 0.50661 7.23982
153 1F76 FMN 0.0006537 0.48061 7.23982
154 1QPR PPC 0.0008916 0.46666 7.23982
155 2FFC U5P 0.000803 0.46473 7.23982
156 2NLI LAC 0.00752 0.43074 7.23982
157 2NLI FMN 0.006473 0.42803 7.23982
158 4GCZ FMN 0.01533 0.40287 7.23982
159 3SXF BK5 0.03815 0.40081 7.23982
160 5SVV FMN 0.01861 0.40053 7.29927
161 1RBL CAP 0.0005606 0.47845 7.33945
162 5FAG PPI 0.005374 0.42292 7.56098
163 4YMZ 13P 0.0000978 0.48625 7.69231
164 3WQD PLP 999 0.002928 0.40096 7.69231
165 5A5W GUO 0.00001607 0.5822 8.1448
166 1PZ1 NAP 0.0223 0.40566 8.1448
167 1U1I NAD 0.03941 0.40112 8.1448
168 2FLI DX5 0.000005209 0.57543 8.18182
169 2V63 CAP 0.0004974 0.479 8.57143
170 2VDH CAP 0.0006099 0.47469 8.57143
171 2V6A CAP 0.0006976 0.46981 8.57143
172 2V68 CAP 0.0004789 0.41054 8.57143
173 1IR2 CAP 0.0004553 0.40404 8.57143
174 2V67 CAP 0.0005623 0.4017 8.57143
175 5TCI MLI 0.0002324 0.42508 8.59729
176 5L4L 7OX 0.03021 0.41012 8.59729
177 1J0D 5PA 0.02354 0.40312 8.59729
178 1UZD CAP 0.0004602 0.48065 8.95522
179 1LBF 137 0.00012 0.51896 9.04977
180 3GLC R5P 0.001186 0.44716 9.04977
181 3PC3 P1T 0.02035 0.42623 9.50226
182 1JXZ BCA 0.01839 0.4112 9.50226
183 1UZH CAP 0.0005456 0.47705 9.83607
184 4Q4K FMN 0.0001971 0.50645 10.4072
185 1TB3 FMN 0.005889 0.43878 10.4072
186 1LYX PGA 0.00003921 0.51973 10.8597
187 3UWV 2PG 0.002076 0.44877 10.8597
188 3T7V MD0 0.004666 0.40673 10.8597
189 3CTL S6P 0.0001129 0.50812 11.3122
190 1W8S FBP 0.002024 0.43871 11.3122
191 3B9O FMN 0.0066 0.41863 11.3122
192 5T79 NDP 0.01915 0.41031 11.7647
193 4JEJ 1GP 0.000006194 0.55433 12.2172
194 2TPS TPS 0.001164 0.46817 12.6697
195 2OO0 PLP 0.00248 0.43685 13.1222
196 3ZNN FAD 0.03964 0.41778 13.1222
197 3ZNN 4WL 0.03964 0.41778 13.1222
198 4JYD SAH 0.01951 0.41117 13.1222
199 2Z6J FMN 0.0004633 0.49296 13.5747
200 1M5W DXP 0.003735 0.4089 13.5747
201 1TRD PGH 0.0000685 0.50532 14
202 4M7T SAM 0.004641 0.42598 14.9321
203 3QH2 3NM 0.00006171 0.48428 15.3846
204 4IXH IMP 0.002357 0.44966 15.8371
205 2Q3R FMN 0.0001913 0.49704 16.2896
206 4BI7 PGA 0.0001298 0.48133 16.2896
207 3AFH GSU 0.01541 0.40091 17.1946
208 2EC9 24X 0.01862 0.40681 36.6667
209 1X1Z BMP 0.00003334 0.5755 40.2715
210 1EIX BMQ 0.00009432 0.50706 41.629
Pocket No.: 2; Query (leader) PDB : 3EXS; Ligand: 5RP; Similar sites found: 48
This union binding pocket(no: 2) in the query (biounit: 3exs.bio2) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1LQA NDP 0.02526 0.40752 1.35747
2 1RC0 KT5 0.03294 0.40271 1.43541
3 5TO8 7FM 0.01273 0.4257 1.80995
4 1QF5 GDP 0.04458 0.40618 1.80995
5 1AFS NAP 0.01007 0.42289 2.26244
6 4D2S DYK 0.005298 0.41216 2.26244
7 3G5D 1N1 0.02186 0.42246 3.16742
8 4ANW O92 0.002409 0.45492 3.61991
9 4O12 2QG 0.03862 0.4368 3.61991
10 1OUK 084 0.04693 0.42718 3.61991
11 4NM5 ADP 0.007131 0.42005 3.61991
12 3EPO MP5 0.009195 0.40949 3.61991
13 3EWC MCF 0.01457 0.40821 3.61991
14 5WGG SAM 0.008319 0.40757 3.61991
15 5UWI GNP 0.0166 0.40688 3.61991
16 5DIF GNP 0.01737 0.40593 3.61991
17 3WG6 NDP 0.02341 0.40349 3.61991
18 5DHF GNP 0.01981 0.40313 3.61991
19 1GVE NAP 0.01544 0.41721 4.0724
20 5BWX 4W4 0.03531 0.40585 4.0724
21 5DXT 5H5 0.01138 0.40511 4.0724
22 4WAS COO 0.03257 0.40395 4.0724
23 1H74 ADP 0.027 0.40391 4.0724
24 5W4W 9WG 0.02647 0.40083 4.0724
25 4U0I 0LI 0.02058 0.40749 4.52489
26 2C5S AMP 0.00462 0.40535 4.52489
27 1QM5 PLP 0.04539 0.40348 4.52489
28 5AWQ GLC GLC 0.03614 0.40128 4.97738
29 4TWP AXI 0.03291 0.40915 5.88235
30 1DJN FMN 0.01701 0.40346 5.88235
31 5ABH YWN 0.01799 0.40227 5.88235
32 1KBI FMN 0.006741 0.45527 6.33484
33 5EOB 5QQ 0.01438 0.43428 6.33484
34 3CY2 MB9 0.0128 0.40785 6.33484
35 3Q9T FAY 0.03771 0.40258 6.33484
36 3EAU PDN 0.03509 0.40229 6.33484
37 2FB3 GTP 0.01923 0.40772 6.78733
38 2FB3 5AD 0.009305 0.40318 6.78733
39 1N4W FAD 0.04419 0.4033 7.69231
40 4NMC 2OP 0.0258 0.40911 8.1448
41 4NMC FAD 0.02696 0.40911 8.1448
42 2C49 ADN 0.00883 0.40839 9.04977
43 1IYK MIM 0.01605 0.41033 9.95475
44 4XH0 ADP 0.01665 0.40263 10.8597
45 1JGT CMA 0.02871 0.40028 12.6697
46 4Z24 FAD 0.03584 0.40723 13.1222
47 3E7O 35F 0.02587 0.40253 13.5747
48 2Y69 CHD 0.01163 0.41088 26.7442
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