Receptor
PDB id Resolution Class Description Source Keywords
2WK9 1.9 Å EC: 2.3.-.- STRUCTURE OF PLP_THR ALDIMINE FORM OF VIBRIO CHOLERAE CQSA VIBRIO CHOLERAE O1 BIOVAR EL TOR OXOAMINE-SYNTHASES PYRIDOXAL PHOSPHATE CQSA CAI-1 TRANSFERASE AUTOINDUCER QUORUM-SENSING ACYLTRANSFERASE AMINOTRANSFERASE
Ref.: INSIGHTS INTO THE BIOSYNTHESIS OF THE VIBRIO CHOLERAE MAJOR AUTOINDUCER CAI-1 FROM THE CRYSTAL STRUCTURE OF THE PLP-DEPENDENT ENZYME CQSA. J.MOL.BIOL. V. 392 763 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PLG B:600;
Valid;
none;
submit data
306.209 C10 H15 N2 O7 P Cc1c(...
PLP A:600;
Valid;
none;
submit data
247.142 C8 H10 N O6 P Cc1c(...
SO4 A:1390;
A:1391;
A:1392;
B:1390;
B:1391;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2WK9 1.9 Å EC: 2.3.-.- STRUCTURE OF PLP_THR ALDIMINE FORM OF VIBRIO CHOLERAE CQSA VIBRIO CHOLERAE O1 BIOVAR EL TOR OXOAMINE-SYNTHASES PYRIDOXAL PHOSPHATE CQSA CAI-1 TRANSFERASE AUTOINDUCER QUORUM-SENSING ACYLTRANSFERASE AMINOTRANSFERASE
Ref.: INSIGHTS INTO THE BIOSYNTHESIS OF THE VIBRIO CHOLERAE MAJOR AUTOINDUCER CAI-1 FROM THE CRYSTAL STRUCTURE OF THE PLP-DEPENDENT ENZYME CQSA. J.MOL.BIOL. V. 392 763 2009
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3KKI - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 2WK9 - PLP C8 H10 N O6 P Cc1c(c(c(c....
3 2WKA - P89 C19 H31 N2 O6 P CCCCCCCCCC....
4 2WK8 - PLP C8 H10 N O6 P Cc1c(c(c(c....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3KKI - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 2WK9 - PLP C8 H10 N O6 P Cc1c(c(c(c....
3 2WKA - P89 C19 H31 N2 O6 P CCCCCCCCCC....
4 2WK8 - PLP C8 H10 N O6 P Cc1c(c(c(c....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3KKI - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 2WK9 - PLP C8 H10 N O6 P Cc1c(c(c(c....
3 2WKA - P89 C19 H31 N2 O6 P CCCCCCCCCC....
4 2WK8 - PLP C8 H10 N O6 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PLG; Similar ligands found: 70
No: Ligand ECFP6 Tc MDL keys Tc
1 PLG 1 1
2 IK2 0.666667 0.890625
3 EA5 0.661972 0.921875
4 PDD 0.651515 0.918033
5 PP3 0.651515 0.918033
6 P1T 0.651515 0.890625
7 PDA 0.651515 0.918033
8 PPD 0.647059 0.966667
9 33P 0.641791 0.901639
10 PLA 0.637681 0.90625
11 5PA 0.632353 0.890625
12 2BK 0.632353 0.918033
13 PLS 0.632353 0.934426
14 TLP 0.632353 0.918033
15 2BO 0.632353 0.918033
16 IN5 0.630769 0.885246
17 C6P 0.623188 0.934426
18 PDG 0.619718 0.935484
19 PGU 0.619718 0.935484
20 PY5 0.614286 0.876923
21 PMG 0.611111 0.878788
22 PL2 0.611111 0.794118
23 76U 0.60274 0.890625
24 KAM 0.597403 0.890625
25 ILP 0.597222 0.888889
26 7XF 0.597222 0.904762
27 CBA 0.597222 0.875
28 PSZ 0.594595 0.808824
29 N5F 0.594595 0.920635
30 QLP 0.589041 0.878788
31 PXP 0.583333 0.8
32 HEY 0.581081 0.90625
33 PY6 0.581081 0.850746
34 PMP 0.57377 0.866667
35 ORX 0.573333 0.890625
36 3LM 0.573333 0.850746
37 PE1 0.565789 0.890625
38 GT1 0.564516 0.746032
39 PMH 0.56338 0.706667
40 PXG 0.551282 0.873016
41 PL4 0.551282 0.890625
42 RW2 0.551282 0.835821
43 7TS 0.533333 0.714286
44 AQ3 0.53012 0.876923
45 DCS 0.526316 0.746667
46 9YM 0.506329 0.818182
47 PL8 0.487805 0.791667
48 PLP ALO 0.48 0.870968
49 1D0 0.476744 0.835821
50 7B9 0.47619 0.826087
51 PLP 2KZ 0.473684 0.84127
52 PLP 0.46875 0.75
53 PLR 0.467742 0.704918
54 P0P 0.454545 0.75
55 PPG 0.452381 0.861538
56 PZP 0.439394 0.754098
57 AN7 0.438356 0.754098
58 CAN PLP 0.433735 0.848485
59 GLY PLP 0.432432 0.85
60 FOO 0.432432 0.790323
61 LCS 0.432099 0.688312
62 2B6 0.426966 0.653846
63 PL6 0.425 0.793651
64 4LM 0.421053 0.738462
65 0JO 0.421053 0.727273
66 GBC PLP 0.418605 0.828125
67 GAB PLP 0.418605 0.828125
68 0LD 0.412371 0.627907
69 KOU 0.410256 0.809524
70 PLP SER 0.402597 0.790323
Ligand no: 2; Ligand: PLP; Similar ligands found: 55
No: Ligand ECFP6 Tc MDL keys Tc
1 PLP 1 1
2 PZP 0.729167 0.843137
3 EXT 0.62069 0.8
4 AN7 0.603448 0.918367
5 EPC 0.603448 0.862745
6 FOO 0.59322 0.849057
7 PLR 0.58 0.895833
8 4LM 0.57377 0.818182
9 0JO 0.57377 0.803571
10 P3D 0.571429 0.704918
11 MPM 0.564516 0.814815
12 KOU 0.555556 0.836364
13 HCP 0.546875 0.77193
14 6DF 0.545455 0.811321
15 PXL 0.541667 0.659574
16 Z98 0.537313 0.75
17 PXP 0.537037 0.862745
18 PMP 0.527273 0.767857
19 P0P 0.527273 0.916667
20 PL6 0.522388 0.818182
21 GT1 0.517857 0.830189
22 PFM 0.514706 0.803571
23 LLP 0.5 0.737705
24 PL5 0.479452 0.775862
25 PUS 0.479452 0.707692
26 MPL 0.473684 0.836364
27 PLG 0.46875 0.75
28 IN5 0.46875 0.758621
29 P89 0.466667 0.714286
30 PLP PUT 0.463768 0.684211
31 5DK 0.460526 0.725806
32 O1G 0.454545 0.75
33 PLP ABU 0.450704 0.706897
34 PLT 0.439024 0.762712
35 X04 0.431034 0.851852
36 PP3 0.426471 0.762712
37 P1T 0.426471 0.714286
38 PDD 0.426471 0.762712
39 PDA 0.426471 0.762712
40 IK2 0.42029 0.714286
41 33P 0.42029 0.745763
42 2BO 0.414286 0.793103
43 PLS 0.414286 0.779661
44 PMH 0.414286 0.619718
45 5PA 0.414286 0.714286
46 TLP 0.414286 0.793103
47 2BK 0.414286 0.793103
48 C6P 0.408451 0.75
49 PPD 0.408451 0.75
50 QLP 0.405405 0.681818
51 MP5 0.403509 0.666667
52 PY5 0.402778 0.703125
53 PLA 0.402778 0.703125
54 HEY 0.4 0.703125
55 PLP PHE 0.4 0.732143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2WK9; Ligand: PLP; Similar sites found: 104
This union binding pocket(no: 1) in the query (biounit: 2wk9.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4RKC PMP 0.005317 0.43242 1.02828
2 5DJ3 5DK 0.004069 0.42644 1.06383
3 1DFO PLG 0.00004589 0.43337 1.79949
4 1C7O PPG 0.007679 0.40759 1.79949
5 3E2Y PMP 0.00004502 0.40142 1.79949
6 1B9I PXG 0.0008042 0.4005 1.80412
7 5TH5 MET 0.04874 0.40011 1.90114
8 2HOX P1T 0.0007266 0.46026 2.05656
9 1XI9 PLP 0.002901 0.45935 2.05656
10 4JE5 PLP 0.004232 0.44603 2.05656
11 4JE5 PMP 0.004259 0.44589 2.05656
12 2ZC0 PMP 0.0003057 0.48197 2.31362
13 1PMO PLR 0.001017 0.47201 2.31362
14 2JFQ DGL 0.02365 0.40814 2.44755
15 3W5N RAM 0.02065 0.42077 2.57069
16 3PD6 PMP 0.0007091 0.48518 2.82776
17 3PDB PMP 0.0008938 0.47478 2.82776
18 5G4J EXT 0.002107 0.43936 2.82776
19 5U23 TQP 0.003065 0.40312 2.87958
20 4ZV1 ARG 0.036 0.40247 3.00429
21 1K2V DEF 0.03082 0.40226 3.00752
22 1GPM AMP 0.01677 0.43895 3.08483
23 1JS3 PLP 142 0.005607 0.42013 3.08483
24 5IWQ PLP 0.004851 0.43856 3.3419
25 1B4N GUA 0.0213 0.41601 3.3419
26 2HHP FLC 0.04305 0.41069 3.3419
27 3B1E P1T 0.01587 0.40945 3.3419
28 2FN1 SAL 0.02842 0.40786 3.3419
29 4JD0 1KH 0.04149 0.40425 3.58566
30 5WYF ILP 0.0006292 0.45885 3.59897
31 2R5E QLP 0.0007584 0.45526 3.59897
32 4FL0 PLP 0.002532 0.45249 3.59897
33 3EI9 PL6 0.004384 0.41197 3.59897
34 1UGY GLA GLC 0.01302 0.43297 3.7594
35 5W70 9YM 0.00003859 0.51251 3.82022
36 4IY7 0JO 0.00002158 0.52367 3.85604
37 4IYO 0JO 0.00002318 0.5223 3.85604
38 4IY7 KOU 0.00002655 0.5197 3.85604
39 4ADC PLP 0.004526 0.41139 3.85604
40 4E1O PLP PVH 0.007245 0.4057 3.85604
41 2XCM ADP 0.01672 0.40835 4.05405
42 4BA5 PXG 0.001468 0.45485 4.11311
43 5DDW 5B6 0.001065 0.44488 4.11311
44 4ZSY RW2 0.00225 0.43077 4.11311
45 1XT8 CYS 0.0174 0.4231 4.11311
46 1LC8 33P 0.0006365 0.43672 4.3956
47 5EXK MET 0.03099 0.41267 4.53172
48 3ZRR PXG 0.0001363 0.48826 4.6875
49 4AZJ SEP PLP 0.0003011 0.4687 4.72222
50 4WXJ GLU 0.03123 0.40971 4.83271
51 5GVL PLG 0.00004385 0.48465 4.88432
52 5GVL GI8 0.00004385 0.48465 4.88432
53 2TPL HPP 0.0004531 0.44598 4.88432
54 4UOX PLP 0.001619 0.46207 5.14139
55 4UOX PUT 0.00537 0.42828 5.14139
56 4UOX PLP PUT 0.006274 0.42141 5.14139
57 4ZAH T5K 0.003887 0.40293 5.14139
58 4ZM4 PLP 0.0005699 0.47916 5.39846
59 1CL2 PPG 0.0002273 0.47842 5.39846
60 4ZM4 P3B 0.004386 0.42149 5.39846
61 3CQ5 PMP 0.0001579 0.53176 5.42005
62 1E5F PLP 0.000001455 0.59632 5.65553
63 1SFF IK2 0.00275 0.43048 5.65553
64 2R2N PMP 0.00185 0.45921 5.9126
65 4K2M O1G 0.0006224 0.45114 5.9126
66 4R5Z PMP 0.0008918 0.44449 5.99455
67 4R5Z SIN 0.001909 0.41496 5.99455
68 3WGC PLG 0.0001471 0.40247 6.15836
69 3BWN PMP 0.0001195 0.51781 6.16967
70 3BWN PMP PHE 0.0007491 0.45152 6.16967
71 1IZO PAM 0.03695 0.40187 6.16967
72 2RC8 DSN 0.00756 0.44362 6.80272
73 1PU7 39A 0.006732 0.41276 6.88073
74 2X5F PLP 0.001042 0.47675 7.19794
75 1VJO PLP 0.0007994 0.46728 7.45501
76 5W71 9YM 0.004021 0.40893 7.45501
77 5W71 PLP 0.0001198 0.40669 7.45501
78 5K8B PDG 0.0001151 0.48235 7.96915
79 1GEX PLP HSA 0.005022 0.40384 8.14607
80 4UHO PLP 0.008282 0.44053 8.99743
81 2FYF PLP 0.00003444 0.55886 9.2545
82 4IMO PWZ 0.04788 0.40099 9.65909
83 1SW1 PBE 0.03086 0.41252 9.81818
84 3VP6 HLD 0.0008485 0.4062 10.0257
85 4E3Q PMP 0.0001233 0.5235 10.2828
86 1H6H PIB 0.02105 0.42188 10.4895
87 1GDE GLU PLP 0.001517 0.44581 11.054
88 4AP9 1PS 0.04025 0.40926 12.4378
89 1UU1 PMP HSA 0.0009605 0.44683 13.7313
90 4WXG 2BO 0.00007057 0.48693 14.2523
91 5G09 6DF 0.001563 0.44135 14.653
92 5X30 4LM 0.000005623 0.56197 15.6812
93 5X30 7XF 0.000004626 0.55943 15.6812
94 5X2Z 3LM 0.00003175 0.45794 15.6812
95 2OAT PFM 0.006208 0.42163 16.4524
96 4AOA IK2 0.000406 0.48114 18.7661
97 2Z9V PXM 0.001539 0.47934 18.7661
98 1M32 PLP 0.0004591 0.50841 18.8525
99 4KQP GLN 0.03209 0.41011 22.4138
100 1GCK ASP PLP 0.0004306 0.46614 22.5974
101 2O66 FLC 0.04748 0.40178 28.1481
102 1FC4 AKB PLP 0.00000004407 0.65069 40.617
103 1DJ9 KAM 0.00000001667 0.68772 40.625
104 2XBN PMP 0.000002197 0.49876 43.9589
Pocket No.: 2; Query (leader) PDB : 2WK9; Ligand: PLG; Similar sites found: 116
This union binding pocket(no: 2) in the query (biounit: 2wk9.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2NLQ GLY 0.02228 0.40263 None
2 4RKC PMP 0.005078 0.43595 1.02828
3 5DJ3 5DK 0.001345 0.45093 1.06383
4 3R4Z GLA 0.0359 0.40932 1.60428
5 1DFO PLG 0.000005018 0.45377 1.79949
6 1C7O PPG 0.01223 0.40413 1.79949
7 5TH5 MET 0.04192 0.40459 1.90114
8 1XI9 PLP 0.001725 0.47375 2.05656
9 2HOX P1T 0.0006584 0.46507 2.05656
10 4JE5 PLP 0.005049 0.44472 2.05656
11 4JE5 PMP 0.005192 0.4441 2.05656
12 3P7I P7I 0.03678 0.40812 2.18069
13 2ZC0 PMP 0.0002911 0.48596 2.31362
14 1PMO PLR 0.0008203 0.47946 2.31362
15 2JFQ DGL 0.02839 0.40638 2.44755
16 2CJH AKG 0.02135 0.40221 2.57069
17 3PD6 PMP 0.0007076 0.48809 2.82776
18 3PDB PMP 0.0008298 0.47921 2.82776
19 5G4J EXT 0.001633 0.4471 2.82776
20 4WCX MET 0.007677 0.43018 2.82776
21 4ZV1 ARG 0.02382 0.41419 3.00429
22 1K2V DEF 0.03226 0.40351 3.00752
23 1JS3 PLP 142 0.004152 0.42863 3.08483
24 5O4F 8VE 0.04296 0.40064 3.10078
25 5IWQ PLP 0.004166 0.44441 3.3419
26 3B1E P1T 0.01631 0.41124 3.3419
27 2YJP CYS 0.03161 0.41082 3.43643
28 5WYF ILP 0.0003568 0.47273 3.59897
29 2R5E QLP 0.0007558 0.45818 3.59897
30 4FL0 PLP 0.00257 0.45484 3.59897
31 3EI9 PL6 0.004199 0.41534 3.59897
32 4NOS H4B 0.0364 0.40986 3.59897
33 4ZYB 4SQ 0.03543 0.40508 3.73134
34 1UGY GLA BGC 0.02053 0.42283 3.7594
35 1UGY GLA GLC 0.01933 0.42131 3.7594
36 5W70 9YM 0.00003885 0.51569 3.82022
37 1DZT ATY 0.02235 0.42072 3.82514
38 4IY7 0JO 0.000004555 0.55723 3.85604
39 4IYO 0JO 0.000004727 0.55651 3.85604
40 4IY7 KOU 0.000005608 0.5532 3.85604
41 4ADC PLP 0.003244 0.42007 3.85604
42 4E1O PLP PVH 0.006249 0.41096 3.85604
43 2XCM ADP 0.01945 0.40751 4.05405
44 3LL9 ADP 0.02066 0.4029 4.08922
45 4BA5 PXG 0.0009201 0.46723 4.11311
46 5DDW 5B6 0.0006288 0.4577 4.11311
47 4ZSY RW2 0.001326 0.44352 4.11311
48 1XT8 CYS 0.02241 0.41936 4.11311
49 1RM8 BAT 0.03078 0.41232 4.14201
50 1LC8 33P 0.0004978 0.44387 4.3956
51 5EXK MET 0.04476 0.40578 4.53172
52 3A9Y CYS 0.03658 0.40825 4.62725
53 3ZRR PXG 0.00004978 0.51089 4.6875
54 4AZJ SEP PLP 0.0001463 0.48542 4.72222
55 4WXJ GLU 0.03904 0.40672 4.83271
56 5GVL GI8 0.00000829 0.50497 4.88432
57 5GVL PLG 0.00000829 0.50497 4.88432
58 2TPL HPP 0.0004184 0.45032 4.88432
59 4UOX PLP 0.0007143 0.48244 5.14139
60 4UOX PUT 0.004038 0.43671 5.14139
61 4UOX PLP PUT 0.007877 0.41933 5.14139
62 4ZAH T5K 0.003241 0.40864 5.14139
63 1WDN GLN 0.0297 0.40914 5.30973
64 1CL2 PPG 0.00007018 0.50424 5.39846
65 4ZM4 PLP 0.0006328 0.47986 5.39846
66 4ZM4 P3B 0.002824 0.43262 5.39846
67 3CQ5 PMP 0.000181 0.53171 5.42005
68 1E5F PLP 0.0000005616 0.61977 5.65553
69 1SFF IK2 0.003944 0.42613 5.65553
70 4JH6 FCN 0.02361 0.41439 5.7971
71 2R2N PMP 0.001888 0.46149 5.9126
72 4K2M O1G 0.0004459 0.46024 5.9126
73 4R5Z PMP 0.0007985 0.44938 5.99455
74 4R5Z SIN 0.001753 0.41913 5.99455
75 3WGC PLG 0.00002893 0.41208 6.15836
76 3BWN PMP 0.000114 0.52198 6.16967
77 3BWN PMP PHE 0.0005812 0.4592 6.16967
78 1IZO PAM 0.03942 0.40262 6.16967
79 5HVJ ANP 0.03552 0.4088 6.34921
80 2RC8 DSN 0.007128 0.4467 6.80272
81 1PU7 39A 0.006227 0.42165 6.88073
82 2X5F PLP 0.001204 0.47637 7.19794
83 1VJO PLP 0.001123 0.46312 7.45501
84 5W71 9YM 0.00502 0.40055 7.45501
85 5K8B PDG 0.0000737 0.49381 7.96915
86 1GEX PLP HSA 0.001684 0.42573 8.14607
87 3SXS PP2 0.009977 0.40809 8.58209
88 4UHO PLP 0.008984 0.44112 8.99743
89 1ELU PDA 0.004991 0.42498 8.99743
90 2FYF PLP 0.00003679 0.5607 9.2545
91 4AML GYU 0.03992 0.40944 9.35672
92 1SW1 PBE 0.0406 0.40768 9.81818
93 3VP6 HLD 0.000346 0.41222 10.0257
94 4E3Q PMP 0.0001422 0.52349 10.2828
95 1GDE GLU PLP 0.001414 0.44995 11.054
96 4LNL 2BO 0.00004457 0.40569 12.012
97 4LNL PLG 0.00004486 0.40234 12.012
98 1OD3 BGC BGC 0.04387 0.40135 13.0952
99 1UU1 PMP HSA 0.0009124 0.45063 13.7313
100 4WXG 2BO 0.00001461 0.51899 14.2523
101 5G09 6DF 0.0006493 0.46112 14.653
102 5X30 4LM 0.000001403 0.59361 15.6812
103 5X30 7XF 0.00000132 0.58787 15.6812
104 5X2Z 3LM 0.000007726 0.46858 15.6812
105 2OAT PFM 0.004526 0.43055 16.4524
106 4YSX MLI 0.02227 0.41842 18.5897
107 4AOA IK2 0.0004102 0.48388 18.7661
108 2Z9V PXM 0.001829 0.47808 18.7661
109 1M32 PLP 0.0005803 0.50597 18.8525
110 4KQP GLN 0.0475 0.40297 22.4138
111 1GCK ASP PLP 0.0003544 0.47286 22.5974
112 1SQL GUN 0.0242 0.41959 23.9726
113 2O66 FLC 0.03602 0.41042 28.1481
114 1FC4 AKB PLP 0.000000001436 0.72276 40.617
115 1DJ9 KAM 0.000000002407 0.73213 40.625
116 2XBN PMP 0.0000006831 0.50202 43.9589
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