Receptor
PDB id Resolution Class Description Source Keywords
1G7V 2.4 Å EC: 2.5.1.55 CRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEXES MECHANISM-BASED INHIBITOR ESCHERICHIA COLI BETA-ALPHA-BARRELS LYASE LIPOPOLYSACCHARIDE
Ref.: CRYSTAL STRUCTURES OF KDOP SYNTHASE IN ITS BINARY C WITH THE SUBSTRATE PHOSPHOENOLPYRUVATE AND WITH A MECHANISM-BASED INHIBITOR. BIOCHEMISTRY V. 40 6326 2001
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PAI A:300;
Valid;
none;
Kd = 0.4 uM
415.225 C9 H23 N O13 P2 C([C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1G7V 2.4 Å EC: 2.5.1.55 CRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEXES MECHANISM-BASED INHIBITOR ESCHERICHIA COLI BETA-ALPHA-BARRELS LYASE LIPOPOLYSACCHARIDE
Ref.: CRYSTAL STRUCTURES OF KDOP SYNTHASE IN ITS BINARY C WITH THE SUBSTRATE PHOSPHOENOLPYRUVATE AND WITH A MECHANISM-BASED INHIBITOR. BIOCHEMISTRY V. 40 6326 2001
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1PHW Ki = 0.5 mM N C5 H11 O7 P C1[C@@H]([....
2 1G7V Kd = 0.4 uM PAI C9 H23 N O13 P2 C([C@H]([C....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1PHW Ki = 0.5 mM N C5 H11 O7 P C1[C@@H]([....
2 1G7V Kd = 0.4 uM PAI C9 H23 N O13 P2 C([C@H]([C....
3 3FYP - PEP C3 H5 O6 P C=C(C(=O)O....
4 3FYO - PEP C3 H5 O6 P C=C(C(=O)O....
50% Homology Family (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1PHW Ki = 0.5 mM N C5 H11 O7 P C1[C@@H]([....
2 1G7V Kd = 0.4 uM PAI C9 H23 N O13 P2 C([C@H]([C....
3 4Z1D - PEP C3 H5 O6 P C=C(C(=O)O....
4 2A2I Kd = 0.04 uM A5P C5 H13 O8 P C([C@H]([C....
5 1LRQ - PEP C3 H5 O6 P C=C(C(=O)O....
6 1ZJI - R5P C5 H11 O8 P C(C(C(C(C=....
7 1FY6 - A5P C5 H13 O8 P C([C@H]([C....
8 3E12 - KD0 C8 H15 O11 P C([C@H]([C....
9 1ZHA Kd = 0.04 uM PEP C3 H5 O6 P C=C(C(=O)O....
10 2NWS Kd = 5.44 uM A5P C5 H13 O8 P C([C@H]([C....
11 1T8X - PEP C3 H5 O6 P C=C(C(=O)O....
12 2NWR - PEP C3 H5 O6 P C=C(C(=O)O....
13 1FXQ - PEP C3 H5 O6 P C=C(C(=O)O....
14 1FWN - PEP C3 H5 O6 P C=C(C(=O)O....
15 1JCY - PEP C3 H5 O6 P C=C(C(=O)O....
16 1LRO - PEP C3 H5 O6 P C=C(C(=O)O....
17 1PCK - PEZ C4 H9 O6 P CCC(C(=O)O....
18 3E0I - PEP C3 H5 O6 P C=C(C(=O)O....
19 2NXG Kd = 17 uM A5P C5 H13 O8 P C([C@H]([C....
20 2NXI - PEP C3 H5 O6 P C=C(C(=O)O....
21 2NX3 Kd = 17 uM A5P C5 H13 O8 P C([C@H]([C....
22 1T96 - PEP C3 H5 O6 P C=C(C(=O)O....
23 2NXH - PEP C3 H5 O6 P C=C(C(=O)O....
24 2EF9 Kd = 14.18 uM A5P C5 H13 O8 P C([C@H]([C....
25 1FWT - E4P C4 H9 O7 P C([C@H]([C....
26 1PE1 - 2PG C3 H7 O7 P C([C@H](C(....
27 2A21 - PEP C3 H5 O6 P C=C(C(=O)O....
28 2NX1 Kd = 0.02 uM RP5 C5 H11 O8 P C([C@@H]1[....
29 1JCX Ki = 7 uM PAI C9 H23 N O13 P2 C([C@H]([C....
30 1FWW - PEP C3 H5 O6 P C=C(C(=O)O....
31 1FWS - PEP C3 H5 O6 P C=C(C(=O)O....
32 1PCW - H4P C7 H19 N O11 P2 C([C@H]([C....
33 3FYP - PEP C3 H5 O6 P C=C(C(=O)O....
34 3FYO - PEP C3 H5 O6 P C=C(C(=O)O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PAI; Similar ligands found: 18
No: Ligand ECFP6 Tc MDL keys Tc
1 PAI 1 1
2 M2P 0.547619 0.767442
3 S6P 0.489362 0.727273
4 AGP 0.45098 0.75
5 M6R 0.45098 0.75
6 G6Q 0.45098 0.727273
7 H4P 0.428571 0.888889
8 KD0 0.418182 0.75
9 6PG 0.415094 0.75
10 LG6 0.415094 0.75
11 R52 0.411765 0.727273
12 R5P 0.411765 0.727273
13 TX4 0.411765 0.673077
14 DX5 0.408163 0.711111
15 A5P 0.408163 0.711111
16 LX1 0.408163 0.688889
17 LXP 0.408163 0.711111
18 I22 0.4 0.733333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1G7V; Ligand: PAI; Similar sites found: 238
This union binding pocket(no: 1) in the query (biounit: 1g7v.bio2) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3KPE TM3 0.001511 0.47639 None
2 4PNO U5P 0.0003554 0.46778 None
3 1C1L GAL BGC 0.01487 0.43414 None
4 1WKL ADP 0.001462 0.43017 None
5 2GJ3 FAD 0.0001469 0.43009 None
6 1UW1 ADP 0.02275 0.41474 None
7 1ZJ6 G3D 0.009387 0.41446 None
8 1WKL ATP 0.005839 0.40775 None
9 4HE2 AMP 0.0002089 0.41941 1.40845
10 3BHO B4P 0.01218 0.45948 1.44231
11 2GWD GLU 0.02057 0.40799 1.76056
12 3QDY CBS 0.04211 0.41137 2.0979
13 1LDM NAD 0.00004432 0.43684 2.11268
14 2QF7 COA 0.002641 0.43275 2.11268
15 1O9U ADZ 0.04043 0.42346 2.11268
16 1HV9 UD1 0.0001547 0.42004 2.11268
17 4QN6 LNV 0.00005446 0.41722 2.11268
18 4KS1 2H8 0.00001586 0.41194 2.11268
19 3A1I UNU 0.0163 0.40835 2.11268
20 4MWV BCZ 0.00006854 0.40531 2.11268
21 2RCN GDP 0.0199 0.40463 2.11268
22 1JH7 UVC 0.008746 0.43418 2.1164
23 4M7F BM3 0.00002705 0.54222 2.21239
24 1J2Z SOG 0.0001902 0.47061 2.22222
25 3RO7 TDR 0.000147 0.4395 2.26415
26 2C2A ADP 0.009766 0.40272 2.32558
27 1NVU GTP 0.0001095 0.41916 2.40964
28 2Q1A 2KT 0.00007892 0.46287 2.46479
29 3ZPG 5GP 0.01179 0.45249 2.46479
30 4HZX G39 0.00001157 0.42816 2.46479
31 1IZC PYR 0.002237 0.41257 2.46479
32 5T63 ALA ALA ALA ALA 0.004047 0.40364 2.46479
33 3TI8 LNV 0.0001292 0.40223 2.46479
34 2Y7G AAE 0.001929 0.43384 2.48227
35 1JN2 SFP 0.03613 0.44505 2.53165
36 1MVQ MMA 0.0008329 0.40196 2.54237
37 1Y9G FRU 0.01889 0.40495 2.7027
38 2H6B 3C4 0.000501 0.40167 2.8
39 4WVH ASP HIS ASP ALA HIS ALA 0.003043 0.44443 2.8169
40 1H0C AOA 0.0197 0.42801 2.8169
41 4L7I SAM 0.004971 0.41394 2.8169
42 4IU0 ABH 0.002078 0.41368 2.8169
43 1JQN DCO 0.0004997 0.40278 2.8169
44 2C9O ADP 0.0006605 0.4021 2.8169
45 5A2J ALA PRO ASP THR ARG PRO 0.008515 0.45636 2.86885
46 2GN2 C5P 0.00005143 0.48972 2.92398
47 4JP3 CIT 0.0001151 0.42057 2.92887
48 3I51 45C 0.00625 0.42178 2.96296
49 2EB5 OXL 0.02751 0.41558 2.99625
50 1ZZ7 S0H 0.01663 0.41644 3.0303
51 2NZ2 ASP 0.0001181 0.51338 3.16901
52 4WBD ADP 0.019 0.42881 3.16901
53 4PB2 5UD 0.003818 0.41463 3.16901
54 1YHM AHD 0.0316 0.40801 3.16901
55 2PP3 LGT 0.001364 0.40551 3.16901
56 2NZ2 CIR 0.002075 0.40123 3.16901
57 3IJH KO2 0.02671 0.41378 3.19635
58 4FUA PGH 0.0003272 0.42663 3.25581
59 4M51 BEZ 0.009013 0.45155 3.27869
60 1YRX FMN 0.01227 0.40586 3.30579
61 2Q37 3AL 0.02956 0.40938 3.31492
62 1ULE GLA GAL NAG 0.04292 0.41621 3.33333
63 3RK0 AMP 0.01976 0.40101 3.37553
64 1F5F DHT 0.006809 0.40872 3.41463
65 4O8A 2OP 0.0022 0.49167 3.52113
66 1I2B UPG 0.0002995 0.44085 3.52113
67 1I2B USQ 0.0002995 0.44085 3.52113
68 1I2B NAD 0.0002995 0.44085 3.52113
69 1WRA PC 0.0115 0.43973 3.52113
70 2OWZ CIT 0.0004243 0.43758 3.52113
71 3U1T MLI 0.02269 0.42493 3.52113
72 1GPJ CIT 0.0298 0.41388 3.52113
73 3MMR ABH 0.001758 0.4065 3.52113
74 4A3R CIT 0.00004913 0.40612 3.52113
75 4NTX AMR 0.03461 0.40399 3.52113
76 2NCD ADP 0.04139 0.40246 3.52113
77 1R6W 164 0.01243 0.40207 3.52113
78 2Q8M AMP 0.0207 0.40017 3.52113
79 3NJQ NJQ 0.00008696 0.44484 3.62694
80 2QLX RM4 0.02027 0.42739 3.7037
81 3R51 MMA 0.03143 0.42943 3.75
82 4B16 NAG 0.007429 0.47154 3.7594
83 1FNZ A2G 0.00008939 0.461 3.79747
84 3U7Y FLC 0.02135 0.45972 3.80952
85 2BLE 5GP 0.000368 0.40861 3.81471
86 4DN8 BMA 0.003543 0.45859 3.84615
87 4LO6 SIA GAL 0.0005873 0.50832 3.87324
88 1RYI GOA 0.046 0.43999 3.87324
89 2VDJ HSE 0.02024 0.4333 3.87324
90 2NLI FMN 0.00004285 0.42588 3.87324
91 2NLI LAC 0.00004285 0.42588 3.87324
92 3GJB AKG 0.01145 0.41919 3.87324
93 2ZJ5 ADP 0.0238 0.41382 3.87324
94 4IV9 TSR 0.01626 0.41365 3.87324
95 1SQ5 PAU 0.03426 0.40211 3.87324
96 3CQ5 PMP 0.03001 0.40072 3.87324
97 2YLD CMO 0.02733 0.41572 3.93701
98 1EYQ NAR 0.00595 0.43168 4.05405
99 4LKK SIA GAL 0.0008827 0.43832 4.16667
100 1Q3Q ANP 0.00001106 0.44756 4.22535
101 4GQB 0XU 0.00002259 0.43525 4.22535
102 1GJW GLC 0.02344 0.42422 4.22535
103 3K3G MMU 0.01551 0.42013 4.22535
104 2IMP NAI 0.0004274 0.41834 4.22535
105 2Q09 DI6 0.01497 0.41408 4.22535
106 2GGH NLQ 0.0001308 0.41306 4.22535
107 1TV5 N8E 0.005673 0.40822 4.22535
108 1JCM 137 0.0001967 0.42667 4.2471
109 1MZV AMP 0.01605 0.40863 4.25532
110 3K9W ADE 0.0002288 0.43389 4.27807
111 3K9W 4PS 0.0002288 0.43389 4.27807
112 1EDO NAP 0.00056 0.40971 4.5082
113 3OIG NAD 0.0002523 0.41302 4.51128
114 1V6A TRE 0.02326 0.41428 4.51807
115 1A5Z OXM 0.00005075 0.56762 4.57746
116 3K37 BCZ 0.00002354 0.45246 4.57746
117 1VCO GLN 0.0008111 0.41414 4.57746
118 2WL9 MBD 0.001427 0.4126 4.57746
119 3NOJ PYR 0.02725 0.40881 4.62185
120 3L6R MLI 0.007427 0.44921 4.62428
121 1T0S BML 0.04459 0.41534 4.65116
122 5DUB GLY 5GG GLY ALA 0.01477 0.44371 4.6729
123 4TMK T5A 0.0002398 0.43957 4.69484
124 1EXB NDP 0.0001968 0.42372 4.85437
125 3SIX GDP 0.002693 0.43691 4.92958
126 3BRE C2E 0.02246 0.41987 4.92958
127 4LCQ URQ 0.0004443 0.41595 4.92958
128 1O0S NAI 0.004071 0.40048 4.92958
129 1NU4 MLA 0.006788 0.48321 5.15464
130 2O66 FLC 0.004688 0.44681 5.18518
131 1LYX PGA 0.00736 0.41482 5.24194
132 4KCT PYR 0.004914 0.43532 5.28169
133 2BO4 FLC 0.01775 0.43029 5.28169
134 1V5F TPP 0.001247 0.42811 5.28169
135 1V5F FAD 0.001247 0.42811 5.28169
136 2VAR AMP 0.007177 0.42356 5.28169
137 3T1A 5MA 0.002731 0.42005 5.28169
138 1T26 NAI 0.0008897 0.41613 5.28169
139 1T26 GBD 0.0008897 0.41613 5.28169
140 3NFZ 3NF 0.01258 0.40917 5.28169
141 2VAR ANP 0.004468 0.40532 5.28169
142 2VAR KDF 0.01971 0.40106 5.28169
143 2JBH 5GP 0.00781 0.42649 5.33333
144 1FX8 BOG 0.004845 0.41437 5.33808
145 1XX4 BAM 0.002278 0.45838 5.36398
146 1JA9 NDP 0.001037 0.40231 5.47445
147 1SJW NGV 0.00003251 0.42299 5.55556
148 4BPM GSH 0.0004163 0.42675 5.61798
149 4Q3S X7A 0.001105 0.41303 5.6338
150 1ONX ASP 0.0009773 0.41158 5.6338
151 1Y42 TYR 0.02315 0.4099 5.6338
152 1ML4 PAL 0.003894 0.40909 5.6338
153 2BGM NAJ 0.0003469 0.40763 5.7554
154 3FPZ AHZ 0.0001923 0.42815 5.82822
155 3TKA CTN 0.006034 0.48976 5.98592
156 1XVA SAM 0.00262 0.41705 5.98592
157 3P7I P7I 0.03594 0.40116 5.98592
158 3QV9 QV7 0.04441 0.40101 5.98592
159 1NXJ GLV 0.002443 0.44861 6.01093
160 1NXJ TLA 0.007979 0.40784 6.01093
161 3Q3C NAD 0.00005369 0.42538 6.02007
162 5DRN 5CT 0.04826 0.42234 6.04651
163 3I8T LBT 0.00009233 0.51821 6.09756
164 3E81 SLB 0.04162 0.40235 6.09756
165 1BDB NAD 0.0001703 0.42547 6.13718
166 1S8F GDP 0.01186 0.40646 6.21469
167 4NVP 7CH 0.00007368 0.40107 6.2201
168 2HMT NAI 0.000007574 0.44313 6.25
169 1H8G CHT 0.01758 0.45891 6.31579
170 1YBH FAD 0.00009202 0.44118 6.33803
171 2P8B NSK 0.0005568 0.42717 6.33803
172 3CKZ ZMR 0.0001411 0.40371 6.33803
173 2Y7P SAL 0.009919 0.42661 6.42202
174 1X1T NAD 0.0008045 0.40672 6.53846
175 2HVK TBA 0.002136 0.46916 6.60377
176 3DUR KDO 0.02779 0.41065 6.61157
177 3EJ0 11X 0.01337 0.4231 6.63265
178 1LTH NAD 0.00009558 0.4188 7.04225
179 2YYJ 4HP 0.001311 0.40575 7.04225
180 2YYJ FAD 0.001311 0.40575 7.04225
181 2J5S KTA 0.001968 0.42536 7.22433
182 2X61 NGA GAL SIA 0.000003812 0.4599 7.36434
183 1GU3 BGC BGC BGC BGC BGC 0.001203 0.46796 7.38255
184 2XDQ MGX 0.002333 0.4903 7.39437
185 3HPF GAE 0.00008957 0.41747 7.39437
186 1Z4V DAN 0.0001483 0.41749 7.74648
187 1OF8 PEP 0.01829 0.40135 7.74648
188 4PTZ FMN 0.006891 0.40852 7.8534
189 4J7H TRH 0.001574 0.42509 8.09859
190 1N6B DMZ 0.0001526 0.40571 8.09859
191 1Y1A GSH 0.01647 0.46364 8.19672
192 1UGX GAL MGC 0.0001456 0.43064 8.27068
193 1JQ5 NAD 0.0008893 0.42809 8.4507
194 4QDC ASD 0.0006066 0.41652 8.4507
195 1GSA GSH 0.00005682 0.4136 8.4507
196 1GSA ADP 0.0001477 0.40986 8.4507
197 1PEA ACM 0.01234 0.44447 8.80282
198 3VGL ANP 0.0002217 0.40153 9.03427
199 2Z5Y HRM 0.0004247 0.41654 9.15493
200 4AF0 MOA 0.001383 0.41306 9.15493
201 1WVC CTP 0.002233 0.40028 9.26641
202 3ZVS MLI 0.03246 0.40627 9.375
203 2ZI8 SDT 0.0004422 0.41601 9.50704
204 4M5P 23W 0.004463 0.46733 9.85915
205 4M5P MLA 0.01077 0.4625 9.85915
206 3CH5 GDP 0.0005099 0.40253 10.1852
207 1SS4 CIT 0.01298 0.48924 10.4575
208 1SS4 GSH 0.005363 0.4862 10.4575
209 4RJK PYR 0.008718 0.47683 10.5634
210 3MAG 3MA 0.0215 0.44558 10.5634
211 4RJK TPP 0.0008524 0.41036 10.5634
212 2V5E SCR 0.001715 0.50718 11
213 4G4S LDZ 0.005764 0.41149 11.1111
214 1F8F NAD 0.0003706 0.40514 11.2676
215 2YCD GTB 0.008717 0.41579 11.3043
216 2JC9 ADN 0.009485 0.42749 11.6197
217 2Q8H TF4 0.03135 0.42949 12.6761
218 3SQG COM 0.009704 0.46503 13.0282
219 1G8S MET 0.03131 0.41284 13.0435
220 4K30 NLG 0.0263 0.40737 13.125
221 3O03 NAP 0.000003899 0.45964 13.3803
222 4OYA 1VE 0.001587 0.41079 13.3803
223 1H16 PYR 0.03932 0.41821 13.7324
224 3VCA PRO 0.02124 0.41383 13.7324
225 3GM5 CIT 0.007217 0.44371 15.7233
226 3S9K CIT 0.006943 0.47772 16.1017
227 4KCF AKM 0.00007837 0.41905 16.9014
228 4KCF FMN 0.00008833 0.40272 16.9014
229 1UO5 PIH 0.02926 0.44583 17.6471
230 3RF4 FUN 0.02313 0.40991 18.1034
231 2OFE NAG 0.003538 0.45862 21.831
232 3SJ0 DXC 0.02532 0.42254 22.5352
233 2XD9 XD9 0.00113 0.42723 23.3533
234 1Y75 NAG 0.01791 0.41065 25.4237
235 1VQ2 DDN 0.0003991 0.40927 36.2694
236 3TFC PEP 0.01244 0.41417 44.3662
237 1RZM E4P 0.005503 0.45571 49.6479
238 1RZM PEP 0.009535 0.42004 49.6479
Pocket No.: 2; Query (leader) PDB : 1G7V; Ligand: PAI; 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: 1g7v.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback