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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: 47
No: Ligand ECFP6 Tc MDL keys Tc
1 5RP 1 1
2 HMS 1 1
3 5SP 1 1
4 XBP 0.657895 0.944444
5 RUB 0.657895 0.944444
6 F6R 0.641026 0.972222
7 TG6 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 GOS 0.5 0.916667
16 P6T 0.5 0.944444
17 2FP 0.5 0.944444
18 M2P 0.5 0.916667
19 P6F 0.5 0.944444
20 LG6 0.488372 0.891892
21 6PG 0.488372 0.891892
22 HG3 0.485714 0.783784
23 PAN 0.466667 0.673469
24 9C2 0.456522 0.66
25 4TP 0.452381 0.75
26 LXP 0.45 0.944444
27 A5P 0.45 0.944444
28 LX1 0.45 0.815789
29 DX5 0.45 0.944444
30 XUL 0.444444 0.638889
31 QDK 0.444444 0.638889
32 RBL 0.444444 0.638889
33 S6P 0.439024 0.916667
34 KD0 0.425532 0.891892
35 E4P 0.425 0.861111
36 5FX 0.421053 0.605263
37 TX4 0.418605 0.632653
38 R5P 0.418605 0.916667
39 R52 0.418605 0.916667
40 DG6 0.418605 0.918919
41 3PG 0.410256 0.837838
42 H4P 0.408163 0.772727
43 52L 0.408163 0.723404
44 DG2 0.404762 0.810811
45 AGP 0.4 0.75
46 G6Q 0.4 0.916667
47 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 with APoc: 277
This union binding pocket(no: 1) in the query (biounit: 3exs.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 3QMN COA None
2 5YRF GLC GLC None
3 5HCY 60D 0.904977
4 4P5E N6P 1.31579
5 4MN7 SME 1.34228
6 5GP0 GPP 1.34228
7 3BW2 FMN 1.35747
8 4JIQ 1L5 1.35747
9 4JIQ FMN 1.35747
10 4D57 ARG AMP 1.35747
11 1VFS DCS 1.80995
12 2XVD AS6 1.80995
13 1KDK DHT 2.25989
14 1OVD ORO 2.26244
15 3W9Z FMN 2.26244
16 2Z6I FMN 2.26244
17 1GTE IUR 2.26244
18 1GTE FMN 2.26244
19 1OVD FMN 2.26244
20 2R14 FMN 2.26244
21 2RJH DCS 2.26244
22 2R14 TXD 2.26244
23 1ZQ5 E04 2.26244
24 1ZQ5 NAP 2.26244
25 1ADO 13P 2.26244
26 3NTY 5P3 2.26244
27 3NTY NAP 2.26244
28 3C5E ATP 2.26244
29 3UXL CFI 2.26244
30 5XVG 8FX 2.26244
31 3AAQ ARU 2.26244
32 2Q3O FMN 2.71493
33 4EWN 0VR 2.71493
34 1UUO FMN 2.71493
35 1UUO BRF 2.71493
36 1UUO ORO 2.71493
37 4QNW FMN 2.71493
38 6BVE PGA 2.71493
39 1BWV CAP 2.71493
40 1UJP CIT 2.71493
41 2GOU FMN 2.71493
42 4M5P FMN 2.71493
43 1NJJ ORX 2.71493
44 2BLE 5GP 2.71493
45 2C6Q NDP 2.71493
46 2C6Q IMP 2.71493
47 5VSM 5AD 2.71493
48 5VSM MET 2.71493
49 6DVH FMN 2.71493
50 6AMI TRP 2.71493
51 6HTO MET 2.71493
52 6HTO 5AD 2.71493
53 6CUZ FEV 2.71493
54 6AM8 PLT 2.71493
55 2Y88 2ER 3.16742
56 1ICP FMN 3.16742
57 1OX5 1PR 3.16742
58 4XP7 FNR 3.16742
59 2F6U CIT 3.16742
60 1OYB HBA 3.16742
61 1OYB FMN 3.16742
62 4TMC FMN 3.16742
63 4TMC HBA 3.16742
64 4NAE 1GP 3.16742
65 3OIX FMN 3.16742
66 4WZH FMN 3.16742
67 4I2D APC 3.16742
68 3CV6 HXS 3.16742
69 3CV6 NAP 3.16742
70 5T9C G3P 3.16742
71 1VJY 460 3.16742
72 1FDJ 13P 3.16742
73 3SJU NDP 3.16742
74 1FDJ 2FP 3.16742
75 3B0P FMN 3.61991
76 2HSA FMN 3.61991
77 2YPI PGA 3.61991
78 5XFV FMN 3.61991
79 2GJN NIS 3.61991
80 1Z44 FMN 3.61991
81 2GJN FMN 3.61991
82 1Z48 FMN 3.61991
83 3ATY FMN 3.61991
84 4CW5 FMN 3.61991
85 1Z42 FMN 3.61991
86 1Z41 FMN 3.61991
87 3C3N FMN 3.61991
88 5YJS SAL 3.61991
89 5OCS FMN 3.61991
90 2HQM FAD 3.61991
91 1PS9 FMN 3.61991
92 1VKF CIT 3.7234
93 1EP2 ORO 4.0724
94 1EP2 FMN 4.0724
95 1PVN MZP 4.0724
96 1AL8 DHP 4.0724
97 1AL8 FMN 4.0724
98 1ME8 RVP 4.0724
99 1JCM 137 4.0724
100 1P4C FMN 4.0724
101 5FI4 5XV 4.0724
102 4WAS COO 4.0724
103 4WAS NAP 4.0724
104 1CSI OAA 4.0724
105 1CSI CMX 4.0724
106 5L9O GOP 4.0724
107 3O84 HTJ 4.0724
108 2F69 SAH 4.0724
109 5N9Z CAP 4.31655
110 5OYA CAP 4.31655
111 5EYW PGA 4.52489
112 5J5R IMP 4.52489
113 5J5R 6G1 4.52489
114 1OFD AKG 4.52489
115 1OFD FMN 4.52489
116 3MJY IJZ 4.52489
117 2H8Z FMN 4.52489
118 2H8Z 8CM 4.52489
119 4I9A NCN 4.52489
120 1TUF AZ1 4.52489
121 3MJY FMN 4.52489
122 2B6N ALA PRO THR 4.52489
123 2VD9 EPC 4.52489
124 2VD9 IN5 4.52489
125 4LUT DCS 4.52489
126 1NIU DCS 4.52489
127 4K38 SAM 4.52489
128 4K39 SAM 4.52489
129 3PDT ADP 4.52489
130 4KXL 6C6 4.60526
131 4HKP TKW 4.80769
132 4HKP 16B 4.80769
133 1CX9 NHP 4.97738
134 3VKC FPQ 4.97738
135 3TAO PGH 4.97738
136 2BTM PGA 4.97738
137 5CSS G3P 4.97738
138 1VHN FMN 4.97738
139 2C91 NAP 4.97738
140 3IS2 FAD 5.19481
141 4OHB 5HM 5.26316
142 1YNQ NDP 5.36278
143 4UTW RFW 5.42986
144 4UTU LRY 5.42986
145 3KRU FMN 5.42986
146 1DBT U5P 5.42986
147 1DQX BMP 5.42986
148 2OEM 1AE 5.42986
149 1VYP TNF 5.42986
150 1VYP FMN 5.42986
151 6BKA FMN 5.42986
152 4YNU LGC 5.42986
153 4YNU FAD 5.42986
154 3HF3 FMN 5.42986
155 4BFM ANP 5.42986
156 3T50 FMN 5.46875
157 2PLK P3D 5.48926
158 1L5Y BEF 5.80645
159 1SW0 PGA 5.88235
160 4Z87 5GP 5.88235
161 5GJO PLP 5.88235
162 4AF0 IMP 5.88235
163 4Z0G 5GP 5.88235
164 2NVA PL2 5.88235
165 4JEM C5P 5.88235
166 4WHZ 3NL 5.88235
167 5DEY 59T 5.88235
168 4UWH JXM 5.88235
169 5N81 8Q2 5.88235
170 5L2R MLA 5.88235
171 3LF0 ATP 6.14035
172 3MI2 PFU 6.33484
173 2QCD U5P 6.33484
174 2Q8Z NUP 6.33484
175 3KDN CAP 6.33484
176 4IGH FMN 6.33484
177 4IGH 1EA 6.33484
178 4IGH ORO 6.33484
179 2RDT 2RD 6.33484
180 2RDT FMN 6.33484
181 3AXK NDP 6.33484
182 1KBI FMN 6.33484
183 1KBI PYR 6.33484
184 5AHN IMP 6.33484
185 1KBJ FMN 6.33484
186 4N02 FNR 6.33484
187 5AHM IMP 6.33484
188 2E7Z MGD 6.33484
189 1NAA ABL 6.33484
190 1NAA 6FA 6.33484
191 1WDD CAP 6.33484
192 1IR1 CAP 6.50407
193 1RBO CAP 6.50407
194 3OVR 5SP 6.78733
195 4A3U FMN 6.78733
196 5AE9 OKO 6.78733
197 3LXN MI1 6.78733
198 4R38 RBF 7.14286
199 1QDS PGA 7.23982
200 4ORM 2V6 7.23982
201 4ORM FMN 7.23982
202 4ORM ORO 7.23982
203 1TV5 FMN 7.23982
204 1F76 FMN 7.23982
205 1QPR PPC 7.23982
206 2FFC U5P 7.23982
207 2NU8 COA 7.23982
208 2NLI FMN 7.23982
209 2NLI LAC 7.23982
210 5BVE 4VG 7.23982
211 1H41 GCV 7.23982
212 4GCZ FMN 7.23982
213 5SVV FMN 7.29927
214 1RBL CAP 7.33945
215 5FAG PPI 7.56098
216 5GVH FMN 7.69231
217 4YMZ 13P 7.69231
218 3WQD PLP 999 7.69231
219 1ZGS XMM 7.69231
220 5A5W GUO 8.1448
221 2ZRU FMN 8.1448
222 1PZ1 NAP 8.1448
223 1U1I NAD 8.1448
224 2FLI DX5 8.18182
225 1IR2 CAP 8.57143
226 2V6A CAP 8.57143
227 2V63 CAP 8.57143
228 2V67 CAP 8.57143
229 2VDH CAP 8.57143
230 1GK8 CAP 8.57143
231 2V68 CAP 8.57143
232 5TCI MLI 8.59729
233 4NJH SAM 8.59729
234 4NJH 2K8 8.59729
235 5L4L 7OX 8.59729
236 1J0D 5PA 8.59729
237 3CW9 01A 8.59729
238 1UZD CAP 8.95522
239 1LBF 137 9.04977
240 3GLC R5P 9.04977
241 2PQ9 GG9 9.04977
242 1JXZ BCA 9.50226
243 5EXK MET 9.50226
244 1UZH CAP 9.83607
245 4Q4K FMN 10.4072
246 1TB3 FMN 10.4072
247 1LYX PGA 10.8597
248 3UWV 2PG 10.8597
249 3T7V MD0 10.8597
250 3CTL S6P 11.3122
251 1W8S FBP 11.3122
252 3B9O FMN 11.3122
253 4RPL 3UC 11.3122
254 4RPL FAD 11.3122
255 1V1A KDG 11.3122
256 5T79 NDP 11.7647
257 4JEJ 1GP 12.2172
258 2TPS TPS 12.6697
259 6GBV FMN 13.0137
260 2OO0 PLP 13.1222
261 3ZNN FAD 13.1222
262 3ZNN 4WL 13.1222
263 4JYD SAH 13.1222
264 2Z6J FMN 13.5747
265 1M5W DXP 13.5747
266 1TRD PGH 14
267 6BFG FMN 14.4796
268 4M7T SAM 14.9321
269 3QH2 3NM 15.3846
270 4IXH IMP 15.8371
271 2Q3R FMN 16.2896
272 4BI7 PGA 16.2896
273 3AFH GSU 17.1946
274 4XZ9 G3P 18.0995
275 1X1Z BMP 40.2715
276 1LOR BMP 40.2715
277 1EIX BMQ 41.629
Pocket No.: 2; Query (leader) PDB : 3EXS; Ligand: 5RP; Similar sites found with APoc: 93
This union binding pocket(no: 2) in the query (biounit: 3exs.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4JGP PYR None
2 2D6M LBT 1.25786
3 1LQA NDP 1.35747
4 1RC0 KT5 1.43541
5 5TO8 7FM 1.80995
6 1QF5 RPL 1.80995
7 1QF5 GDP 1.80995
8 6ES0 BW8 1.89274
9 5EH0 5NW 2.26244
10 5WS9 OXL 2.26244
11 1AFS NAP 2.26244
12 5WS9 ATP 2.26244
13 5D4Y BXP 2.26244
14 2P53 NNG 2.71493
15 3G5D 1N1 3.16742
16 2HZY DHJ 3.16742
17 3WV6 GAL BGC 3.16742
18 6C1S EFV 3.61991
19 4O12 2QG 3.61991
20 1OUK 084 3.61991
21 2PNC CLU 3.61991
22 3EPO MP5 3.61991
23 3EWC MCF 3.61991
24 2GVJ DGB 3.61991
25 5WGG SAM 3.61991
26 5UWI GNP 3.61991
27 6CIT GNP 3.61991
28 5DIF GNP 3.61991
29 4IP7 FLC 3.61991
30 5UWJ GNP 3.61991
31 3WG6 NDP 3.61991
32 5DHF GNP 3.61991
33 6G5Q EMZ 3.61991
34 1GVE NAP 4.0724
35 5BJX NAD 4.0724
36 5BJX UDP 4.0724
37 5I60 67W 4.0724
38 5DXT 5H5 4.0724
39 2G50 PYR 4.0724
40 1H74 ADP 4.0724
41 5V1B 8UY 4.0724
42 5ZI9 FLC 4.0724
43 4KBA 1QM 4.0724
44 5U97 PIT 4.0724
45 2C5S AMP 4.52489
46 3U6W KIV 4.52489
47 4U0I 0LI 4.52489
48 1QM5 PLP 4.52489
49 5OKT 9XK 4.52489
50 2GMH FAD 4.97738
51 5AWM ANP 4.97738
52 5AWQ GLC GLC 4.97738
53 5DG2 GAL GLC 5.18518
54 3D72 FAD 5.36913
55 2BP1 NDP 5.42986
56 2VN9 GVD 5.42986
57 3HB5 E2B 5.42986
58 3GAY P6T 5.42986
59 4TWP AXI 5.88235
60 3TY5 ATP 5.88235
61 1DJN FMN 5.88235
62 4DC2 ADE 5.88235
63 5ABH YWN 5.88235
64 5EOB 5QQ 6.33484
65 3CY2 MB9 6.33484
66 3Q9T FAY 6.33484
67 3EAU PDN 6.33484
68 3EAU NDP 6.33484
69 5XHA FRU 6.78733
70 2FB3 GTP 6.78733
71 2FB3 5AD 6.78733
72 1ZXM ANP 7.23982
73 5Y86 HRM 7.69231
74 4NMC 2OP 8.1448
75 4NMC FAD 8.1448
76 5CIC 51R 8.33333
77 2C49 ADN 9.04977
78 1IYK MIM 9.95475
79 2YMZ LAT 10
80 4XH0 ADP 10.8597
81 5OC1 FAD 11.3122
82 4JTA NAP 11.7647
83 3OYW TDG 11.9403
84 1W6O LAT 11.9403
85 1JGT CMA 12.6697
86 1A78 TDG 12.6866
87 4Z24 FAD 13.1222
88 1IGW PYR 13.1222
89 3E7O 35F 13.5747
90 2JK0 ASP 14.4796
91 3N9R TD3 14.9321
92 2Y69 CHD 26.7442
93 1QKQ MAN 33.0986
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