Receptor
PDB id Resolution Class Description Source Keywords
4NAE 2 Å EC: 2.5.1.- PCRB FROM GEOBACILLUS KAUSTOPHILUS, WITH BOUND G1P GEOBACILLUS KAUSTOPHILUS PCRB GGGP TRANSFERASE
Ref.: A COMPREHENSIVE ANALYSIS OF THE GERANYLGERANYLGLYCE PHOSPHATE SYNTHASE ENZYME FAMILY IDENTIFIES NOVEL M AND REVEALS MECHANISMS OF SUBSTRATE SPECIFICITY AND QUATERNARY STRUCTURE ORGANIZATION. MOL.MICROBIOL. V. 92 885 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PE4 A:302;
B:302;
Invalid;
Invalid;
none;
none;
submit data
354.436 C16 H34 O8 CCOCC...
1GP A:301;
B:301;
Valid;
Valid;
none;
none;
submit data
172.074 C3 H9 O6 P C([C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4NAE 2 Å EC: 2.5.1.- PCRB FROM GEOBACILLUS KAUSTOPHILUS, WITH BOUND G1P GEOBACILLUS KAUSTOPHILUS PCRB GGGP TRANSFERASE
Ref.: A COMPREHENSIVE ANALYSIS OF THE GERANYLGERANYLGLYCE PHOSPHATE SYNTHASE ENZYME FAMILY IDENTIFIES NOVEL M AND REVEALS MECHANISMS OF SUBSTRATE SPECIFICITY AND QUATERNARY STRUCTURE ORGANIZATION. MOL.MICROBIOL. V. 92 885 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4NAE - 1GP C3 H9 O6 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 6 families.
1 4NAE - 1GP C3 H9 O6 P C([C@@H](C....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2F6U - CIT C6 H8 O7 C(C(=O)O)C....
2 2F6X - 1GP C3 H9 O6 P C([C@@H](C....
3 4NAE - 1GP C3 H9 O6 P C([C@@H](C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 1GP; Similar ligands found: 25
No: Ligand ECFP6 Tc MDL keys Tc
1 1GP 1 1
2 G3P 1 1
3 GP9 0.551724 0.90625
4 GPE 0.514286 0.731707
5 M2P 0.5 0.882353
6 LX1 0.484848 0.828571
7 A5P 0.484848 0.911765
8 DX5 0.484848 0.911765
9 LXP 0.484848 0.911765
10 HG3 0.482759 0.90625
11 S6P 0.470588 0.939394
12 DXP 0.457143 0.828571
13 G3H 0.4375 0.848485
14 3PG 0.4375 0.852941
15 D5X 0.432432 0.805556
16 CH5 0.425 0.6
17 EFS 0.423077 0.69697
18 M6R 0.421053 0.756098
19 AGP 0.421053 0.756098
20 GSE 0.414634 0.714286
21 E4P 0.411765 0.878788
22 R5P 0.405405 0.828571
23 DG6 0.405405 0.885714
24 TX4 0.405405 0.630435
25 R52 0.405405 0.828571
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4NAE; Ligand: 1GP; Similar sites found: 322
This union binding pocket(no: 1) in the query (biounit: 4nae.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2X4Z X4Z 0.01311 0.43327 None
2 4J6W CTP 0.02386 0.41579 None
3 2RHO GSP 0.02179 0.41252 None
4 1L1Q 9DA 0.02227 0.40713 1.6129
5 1U72 MTX 0.0401 0.41941 2.15054
6 1U72 NDP 0.0401 0.41941 2.15054
7 3OIX FMN 0.0002869 0.51629 2.22222
8 2WW4 ADP 0.00191 0.45472 2.22222
9 1LVL FAD 0.009173 0.45218 2.22222
10 3EYA TDP 0.01925 0.41492 2.22222
11 3EYA FAD 0.03869 0.41356 2.22222
12 1OYB HBA 0.000273 0.52231 2.66667
13 1OYB FMN 0.0002169 0.52231 2.66667
14 3KDN CAP 0.0008322 0.51701 2.66667
15 3ATY FMN 0.001636 0.47516 2.66667
16 4CW5 FMN 0.0013 0.46656 2.66667
17 5EW9 5VC 0.04031 0.44019 2.66667
18 5XDT MB3 0.01761 0.42713 2.66667
19 5XDT GDP 0.01429 0.42508 2.66667
20 2BP1 NDP 0.02241 0.4194 2.66667
21 1V35 NAI 0.0301 0.41861 2.66667
22 4C3Y ANB 0.03797 0.41705 2.66667
23 4YNU FAD 0.04742 0.41027 2.66667
24 2RGJ FAD 0.03641 0.40881 2.66667
25 5IXJ THR 0.0338 0.40812 2.66667
26 1YNQ NDP 0.03179 0.40694 2.66667
27 2FJK 13P 0.00177 0.40524 2.66667
28 1MVN FMN 0.01609 0.42021 2.87081
29 5CSS G3P 0.00002045 0.54639 3.09735
30 2HSA FMN 0.0002902 0.52173 3.11111
31 4EWN 0VR 0.0001211 0.51759 3.11111
32 2Q3O FMN 0.0004369 0.50344 3.11111
33 2TPS TPS 0.0006829 0.49502 3.11111
34 2OO0 PLP 0.0005287 0.47745 3.11111
35 4LUT DCS 0.004125 0.44467 3.11111
36 4RGQ 13P 0.01316 0.43907 3.11111
37 1ADO 13P 0.006487 0.43739 3.11111
38 1FDJ 2FP 0.003187 0.43713 3.11111
39 3G5S FAD 0.01874 0.43232 3.11111
40 4RGQ NDP 0.01696 0.42493 3.11111
41 1LQA NDP 0.01777 0.42373 3.11111
42 3UBM COA 0.01867 0.4169 3.11111
43 2G50 PYR 0.0236 0.41547 3.11111
44 1ZK7 FAD 0.03818 0.4153 3.11111
45 1FL2 FAD 0.03865 0.41419 3.11111
46 1V7C HEY 0.03219 0.41083 3.11111
47 3NTY NAP 0.04998 0.4086 3.11111
48 3OZG SSI 0.01815 0.40761 3.11111
49 1FDJ 13P 0.009533 0.40431 3.11111
50 4JWH SAH 0.03807 0.40333 3.11111
51 3EXS 5RP 0.0001153 0.51371 3.16742
52 1VKF CIT 0.002149 0.4212 3.19149
53 1HDO NAP 0.04774 0.40729 3.39806
54 3TAO PGH 0.000007256 0.56956 3.55556
55 1TRD PGH 0.0000246 0.54544 3.55556
56 4BI7 PGA 0.00003324 0.53555 3.55556
57 1JCM 137 0.00009691 0.52962 3.55556
58 1ICP FMN 0.0002266 0.52906 3.55556
59 1OFD FMN 0.0005268 0.51337 3.55556
60 1OFD AKG 0.001162 0.49395 3.55556
61 2PLK P3D 0.0005224 0.48824 3.55556
62 1DBT U5P 0.0008065 0.48323 3.55556
63 1F76 FMN 0.002462 0.46772 3.55556
64 1RC0 KT5 0.003279 0.46115 3.55556
65 1N4W FAD 0.02129 0.42937 3.55556
66 1D4D FAD 0.02308 0.42612 3.55556
67 3MN6 ATP 0.01158 0.42322 3.55556
68 3CV6 NAP 0.02576 0.42198 3.55556
69 3CV6 HXS 0.02673 0.42198 3.55556
70 3AB1 FAD 0.03315 0.41883 3.55556
71 3FGC FMN 0.02221 0.40688 3.55556
72 2Q28 ADP 0.02726 0.4065 3.55556
73 3P7N FMN 0.02187 0.40606 3.55556
74 1OSS BEN 0.01311 0.402 3.58744
75 1P18 7HP 0.01617 0.41769 3.61991
76 4N1T 2GD 0.0484 0.4034 3.77358
77 1LBF 137 0.00003791 0.56951 4
78 1DQX BMP 0.0001359 0.52612 4
79 4ORM 2V6 0.001151 0.52128 4
80 4ORM ORO 0.001151 0.52128 4
81 4ORM FMN 0.001151 0.52128 4
82 4XP7 FNR 0.0005547 0.48768 4
83 2D1S SLU 0.01402 0.42667 4
84 2A8X FAD 0.0308 0.4238 4
85 5F3I 5UJ 0.0303 0.40957 4
86 2XGT NSS 0.03459 0.40773 4
87 5CUQ NSC 0.04985 0.40261 4
88 2FLI DX5 0.0001741 0.52006 4.09091
89 5GM9 CBK 0.03618 0.40582 4.22535
90 5DYO FLU 0.008808 0.40617 4.24528
91 3AIA SAM 0.01735 0.40751 4.2654
92 3LXK MI1 0.01851 0.42386 4.28135
93 4EES FMN 0.02109 0.40706 4.34783
94 3MI2 PFU 0.0006846 0.5212 4.44444
95 1EP2 FMN 0.0003592 0.51894 4.44444
96 1EP2 ORO 0.0005164 0.51894 4.44444
97 4HKP 16B 0.0001634 0.51696 4.44444
98 4HKP TKW 0.0002143 0.51682 4.44444
99 2QCD U5P 0.0002266 0.51211 4.44444
100 4I9A NCN 0.0001796 0.50962 4.44444
101 1Z48 FMN 0.0008179 0.4755 4.44444
102 1Z41 FMN 0.001004 0.47315 4.44444
103 3B9O FMN 0.003061 0.44878 4.44444
104 4USQ FAD 0.03686 0.43539 4.44444
105 3OV6 MK0 0.01921 0.42427 4.44444
106 1UWK NAD 0.03432 0.41837 4.44444
107 1UWK URO 0.03432 0.41837 4.44444
108 1JG3 ADN 0.02558 0.41771 4.44444
109 1M5W DXP 0.009569 0.41159 4.44444
110 1ZK4 NAP 0.04455 0.40424 4.44444
111 5FAG PPI 0.01891 0.40297 4.44444
112 1NE7 AGP 0.01909 0.4019 4.44444
113 3BC9 G6D GLC ACI GLD GLC ACI GLD GLC BGC 0.04778 0.4011 4.44444
114 1PJS NAD 0.02498 0.40088 4.44444
115 3O3R NAP 0.03956 0.40011 4.44444
116 5FUI APY 0.00288 0.40107 4.54545
117 1AL8 FMN 0.00007042 0.5443 4.88889
118 1AL8 DHP 0.0001112 0.5443 4.88889
119 2YPI PGA 0.00001045 0.49223 4.88889
120 4YMZ 13P 0.00003841 0.47915 4.88889
121 2BLE 5GP 0.001715 0.47266 4.88889
122 1RP0 AHZ 0.006749 0.44579 4.88889
123 1NJJ ORX 0.0052 0.43825 4.88889
124 2RJH DCS 0.005441 0.43511 4.88889
125 4B1W ATP 0.008357 0.43373 4.88889
126 1XDY MTE 0.007768 0.43222 4.88889
127 3LM9 FRU 0.01848 0.41904 4.88889
128 1VGR COA 0.02514 0.41855 4.88889
129 2VJM COA 0.01912 0.41732 4.88889
130 1V25 ANP 0.02834 0.41719 4.88889
131 4O8A FAD 0.02427 0.41691 4.88889
132 3B4Y F42 0.02462 0.40638 4.88889
133 2VJJ RAM GLC GAL NAG NAG GLC 0.04581 0.40401 4.88889
134 2Q0L NAP 0.01699 0.403 4.88889
135 4JWF SAH 0.03122 0.40372 5.06912
136 3HF3 FMN 0.002743 0.45894 5.15759
137 1UHK CZN 0.02192 0.41614 5.2356
138 4Q4K FMN 0.000007706 0.5978 5.33333
139 2BTM PGA 0.00002204 0.54538 5.33333
140 1KBJ FMN 0.00008671 0.54457 5.33333
141 1KBI PYR 0.0001091 0.53937 5.33333
142 3WQT ANP 0.01045 0.42702 5.33333
143 5EYP GTP 0.03037 0.40687 5.33333
144 4D9C PMP 0.03734 0.40041 5.33333
145 3NZ1 3NY 0.01215 0.40028 5.36398
146 3AXK NDP 0.0166 0.40955 5.42636
147 1WDD CAP 0.000233 0.51574 5.46875
148 1GAR U89 0.002787 0.46761 5.66038
149 1RBO CAP 0.002828 0.52514 5.69106
150 1IR1 CAP 0.0002239 0.51676 5.69106
151 1L3I SAH 0.02808 0.40714 5.72917
152 1QDS PGA 0.000008519 0.56801 5.77778
153 3C3N FMN 0.0005269 0.51911 5.77778
154 2VD9 EPC 0.006969 0.43235 5.77778
155 2VD9 IN5 0.006377 0.43235 5.77778
156 1W8S FBP 0.004936 0.43218 5.77778
157 3LU1 NAD 0.01257 0.42809 5.77778
158 5KF6 FAD 0.02405 0.41721 5.77778
159 5KF6 TFB 0.02405 0.41721 5.77778
160 3CTY FAD 0.04532 0.4134 5.77778
161 2JBH 5GP 0.01021 0.41255 5.77778
162 3GCZ SAM 0.02361 0.40598 5.77778
163 3LKZ SFG 0.02439 0.40549 5.77778
164 1O5O U5P 0.01046 0.41526 5.88235
165 1UZD CAP 0.0001729 0.52352 6.22222
166 5EYW PGA 0.00004151 0.47851 6.22222
167 1PVN MZP 0.003363 0.47027 6.22222
168 1ME8 RVP 0.005593 0.4532 6.22222
169 3GLC R5P 0.002365 0.44677 6.22222
170 1TDF NAP 0.03303 0.43534 6.22222
171 1Z2I NAD 0.01614 0.42483 6.22222
172 1TDF FAD 0.0382 0.4168 6.22222
173 1SOX MTE 0.02635 0.40174 6.22222
174 1RBL CAP 0.0002037 0.52358 6.42202
175 1XTT U5P 0.003878 0.44407 6.48148
176 2YKL NLD 0.01827 0.40361 6.48148
177 1HGX 5GP 0.003953 0.43117 6.55738
178 1TB3 FMN 0.0002946 0.52062 6.66667
179 4JIQ 1L5 0.0005117 0.50361 6.66667
180 4JIQ FMN 0.0005117 0.50361 6.66667
181 1UUO BRF 0.002502 0.49542 6.66667
182 1UUO ORO 0.002352 0.49542 6.66667
183 1PS9 FMN 0.005742 0.44168 6.66667
184 1HDR NAD 0.04873 0.41557 6.66667
185 2VVM FAD 0.04368 0.41171 6.66667
186 1X54 4AD 0.03509 0.40471 6.66667
187 5A5W GUO 0.000009649 0.61751 7.11111
188 2RDT 2RD 0.0001427 0.5406 7.11111
189 2RDT FMN 0.0001002 0.5406 7.11111
190 1GTE FMN 0.000292 0.5298 7.11111
191 1VYP TNF 0.0002718 0.51741 7.11111
192 1VYP FMN 0.0002932 0.51741 7.11111
193 4N02 FNR 0.002362 0.4669 7.11111
194 4A3U FMN 0.002542 0.45921 7.11111
195 5TPR NAD 0.03026 0.41311 7.11111
196 1GY8 NAD 0.03934 0.40716 7.11111
197 3W9Z FMN 0.00003016 0.55765 7.55556
198 3C56 PH4 0.003559 0.44528 7.55556
199 3N9R TD3 0.002133 0.44096 7.55556
200 3PGU OLA 0.01378 0.40696 7.55556
201 3LL5 IPE 0.03725 0.40606 7.55556
202 1VHN FMN 0.01694 0.40546 7.55556
203 2PHN GDP 0.03239 0.40002 7.55556
204 5ALC TIQ 0.006224 0.44526 7.69231
205 1UJP CIT 0.00002447 0.44102 7.74908
206 1ZN7 PRP 0.02014 0.41086 7.77778
207 1ZN7 ADE 0.01369 0.40966 7.77778
208 4UTU LRY 0.00001533 0.56606 8
209 2NVA PL2 0.0001687 0.52229 8
210 4UTW RFW 0.00002094 0.44205 8
211 3A1I UNU 0.01199 0.40638 8
212 3GFZ C2E 0.0311 0.40566 8
213 2VBU CDP 0.03505 0.40726 8.08823
214 2GAG NAD 0.02563 0.42086 8.09524
215 2FXV 5GP 0.03294 0.4032 8.24742
216 3RFV NAI 0.0471 0.40041 8.37004
217 3NCQ ATP 0.03148 0.40086 8.40336
218 4IGH FMN 0.001372 0.51737 8.44444
219 4IGH 1EA 0.001372 0.51737 8.44444
220 4IGH ORO 0.001372 0.51737 8.44444
221 4AF0 IMP 0.0003024 0.50622 8.44444
222 5GJO PLP 0.0007114 0.469 8.44444
223 1GVE NAP 0.004427 0.45897 8.44444
224 2OEM 1AE 0.004558 0.43376 8.44444
225 3H0L ADP 0.003423 0.43173 8.44444
226 1FS5 TLA 0.007892 0.42619 8.44444
227 2C91 NAP 0.01875 0.42355 8.44444
228 3L9R L9Q 0.02554 0.42098 8.44444
229 3L9R L9R 0.0387 0.41388 8.44444
230 3U4C NDP 0.0435 0.40129 8.44444
231 4NAT 2W5 0.04583 0.4049 8.75
232 2Q3R FMN 0.0006721 0.48804 8.81057
233 3UWV 2PG 0.0001111 0.53 8.88889
234 4IXH IMP 0.0003846 0.50148 8.88889
235 1B57 PGH 0.001299 0.4566 8.88889
236 3EAU PDN 0.0135 0.43597 8.88889
237 4JTA NAP 0.01235 0.43522 8.88889
238 1ZFJ IMP 0.006561 0.43211 8.88889
239 1DJN FMN 0.02982 0.40301 8.88889
240 1GRN AF3 0.01585 0.40054 8.90052
241 2I8T GDD 0.01444 0.42466 8.98204
242 2Z6I FMN 0.00002814 0.4087 9.03614
243 4NMC FAD 0.02676 0.42034 9.2511
244 4NMC 2OP 0.02574 0.42034 9.2511
245 3CQ5 PMP 0.01127 0.40376 9.2511
246 1LYX PGA 0.000006216 0.57786 9.33333
247 2B4G FMN 0.00002858 0.5771 9.33333
248 1PZ1 NAP 0.006619 0.44478 9.33333
249 3O84 HTJ 0.007112 0.44261 9.33333
250 2BKX F6R 0.004656 0.43477 9.33333
251 2G37 FAD 0.007989 0.42895 9.33333
252 1Q6O LG6 0.0007317 0.47575 9.72222
253 3B0P FMN 0.000008155 0.58412 9.77778
254 2SFP PPI 0.007875 0.42743 9.77778
255 4H6Q FAD 0.01165 0.42732 9.77778
256 4H6Q TFB 0.01377 0.42732 9.77778
257 3PJU C2E 0.03594 0.40514 9.77778
258 1QSM ACO 0.03265 0.40724 9.86842
259 5C9J STE 0.01746 0.41392 10.101
260 3CTL S6P 0.01431 0.41644 10.1322
261 1QPR PPC 0.00309 0.45146 10.2222
262 3IES M24 0.01149 0.43745 10.2222
263 2NLI LAC 0.01647 0.4238 10.2222
264 2NLI FMN 0.01559 0.4238 10.2222
265 2HJR APR 0.02957 0.40156 10.2222
266 2Q8Z NUP 0.0008619 0.48405 10.6667
267 4QNW FMN 0.00102 0.48052 10.6667
268 5C5H 4YB 0.04013 0.40096 10.6667
269 1GVF PGH 0.0004674 0.47283 11.0132
270 3MJY FMN 0.00004782 0.57322 11.1111
271 3MJY IJZ 0.00004782 0.57322 11.1111
272 5UAO FAD 0.04772 0.4093 11.1111
273 3QFA FAD 0.04695 0.4153 11.2069
274 1TUF AZ1 0.0004092 0.49994 11.5556
275 4M5P FMN 0.0005389 0.49728 11.5556
276 4J7H TLO 0.02496 0.41013 11.5556
277 3ICT ADP 0.01833 0.40258 11.5556
278 4O9S 2RY 0.01242 0.42862 11.6279
279 1BWV CAP 0.0002183 0.51543 12
280 2FFC U5P 0.01122 0.42243 12
281 3HQP OXL 0.01188 0.41916 12
282 3SXF BK5 0.04037 0.40753 12
283 1X1Z BMP 0.001217 0.50713 12.3016
284 3WG6 NDP 0.02022 0.42104 12.4444
285 4Q9N NAI 0.02425 0.4177 12.4444
286 1AOE GW3 0.02463 0.42129 12.5
287 2F5Z FAD 0.04731 0.40868 12.5
288 2GOU FMN 0.0008298 0.50116 12.8889
289 1BC5 ACE ASN TRP GLU THR PHE 0.00839 0.41128 12.8889
290 3BW2 FMN 0.000008036 0.60661 13.0081
291 1ERB ETR 0.02303 0.4171 13.1148
292 3QH2 3NM 0.00008258 0.51442 13.1222
293 3OVR 5SP 0.0003556 0.50673 13.3333
294 4OXI GAP 0.02573 0.40685 13.7778
295 5KJW 53C 0.009302 0.40448 14.6667
296 1P4C FMN 0.009863 0.43583 15.1111
297 3QFU ADP 0.02477 0.40229 15.1111
298 1EXB NDP 0.01036 0.43954 15.534
299 2Z6J FMN 0.00003263 0.57086 16
300 2Y88 2ER 0.00001312 0.60522 16.4444
301 2QIA U20 0.02468 0.42148 16.8889
302 3N39 FMN 0.03578 0.40138 17.3333
303 5UKL SIX 0.02879 0.40871 17.7419
304 4A62 ANP 0.01629 0.41662 17.7778
305 1OVD FMN 0.00003757 0.58619 20
306 1OVD ORO 0.00003757 0.58619 20
307 2C6Q IMP 0.000391 0.50399 20
308 2C6Q NDP 0.001639 0.49083 20
309 1EIX BMQ 0.001693 0.46245 20
310 1UZH CAP 0.0002197 0.51977 20.4918
311 5C2N NAG 0.002913 0.42054 20.8333
312 2V63 CAP 0.000168 0.52551 21.4286
313 2VDH CAP 0.0001835 0.52332 21.4286
314 2V67 CAP 0.0002207 0.51913 21.4286
315 2V6A CAP 0.0002132 0.51786 21.4286
316 3CQD ATP 0.01829 0.42684 22.6667
317 1NZY BCA 0.006843 0.44069 23.1111
318 1SW0 PGA 0.000009919 0.56831 29.7778
319 3KRU FMN 0.0005937 0.51115 30.837
320 3VKC FPQ 0.00003462 0.56028 32.1678
321 5TCI MLI 0.00003521 0.50704 40.4444
322 4JEJ 1GP 0.00000004635 0.69072 41.3333
Pocket No.: 2; Query (leader) PDB : 4NAE; Ligand: 1GP; 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: 4nae.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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