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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 TRANSFAUTOINDUCER QUORUM-SENSING ACYLTRANSFERASE AMINOTRANSFER
Ref.: INSIGHTS INTO THE BIOSYNTHESIS OF THE VIBRIO CHOLER 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 TRANSFAUTOINDUCER QUORUM-SENSING ACYLTRANSFERASE AMINOTRANSFER
Ref.: INSIGHTS INTO THE BIOSYNTHESIS OF THE VIBRIO CHOLER 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: 74
No: Ligand ECFP6 Tc MDL keys Tc
1 PLG 1 1
2 IK2 0.666667 0.890625
3 EA5 0.661972 0.921875
4 PDA 0.651515 0.918033
5 PP3 0.651515 0.918033
6 PDD 0.651515 0.918033
7 P1T 0.651515 0.890625
8 PPD 0.647059 0.966667
9 33P 0.641791 0.901639
10 PLA 0.637681 0.90625
11 TLP 0.632353 0.918033
12 5PA 0.632353 0.890625
13 2BK 0.632353 0.918033
14 PLS 0.632353 0.934426
15 2BO 0.632353 0.918033
16 IN5 0.630769 0.885246
17 C6P 0.623188 0.934426
18 PGU 0.619718 0.935484
19 PDG 0.619718 0.935484
20 PY5 0.614286 0.876923
21 PL2 0.611111 0.794118
22 PMG 0.611111 0.878788
23 76U 0.60274 0.890625
24 KAM 0.597403 0.890625
25 CBA 0.597222 0.875
26 7XF 0.597222 0.904762
27 ILP 0.597222 0.888889
28 N5F 0.594595 0.920635
29 PSZ 0.594595 0.808824
30 QLP 0.589041 0.878788
31 LPI 0.589041 0.865672
32 PXP 0.583333 0.8
33 HEY 0.581081 0.90625
34 PY6 0.581081 0.850746
35 PMP 0.57377 0.866667
36 ORX 0.573333 0.890625
37 3LM 0.573333 0.850746
38 PE1 0.565789 0.890625
39 GT1 0.564516 0.746032
40 PMH 0.56338 0.706667
41 PXG 0.551282 0.873016
42 PL4 0.551282 0.890625
43 RW2 0.551282 0.835821
44 7TS 0.533333 0.714286
45 AQ3 0.53012 0.876923
46 DCS 0.526316 0.746667
47 9YM 0.506329 0.818182
48 PL8 0.487805 0.791667
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 RMT 0.447059 0.776119
57 EVM 0.441558 0.796875
58 PZP 0.439394 0.754098
59 AN7 0.438356 0.754098
60 DOW 0.434343 0.838235
61 FOO 0.432432 0.790323
62 LCS 0.432099 0.688312
63 CAN PLP 0.428571 0.835821
64 FEV 0.428571 0.727273
65 2B6 0.426966 0.653846
66 PL6 0.425 0.793651
67 4LM 0.421053 0.738462
68 0JO 0.421053 0.727273
69 GBC PLP 0.418605 0.828125
70 GAB PLP 0.418605 0.828125
71 F0G 0.415584 0.774194
72 0LD 0.412371 0.627907
73 KOU 0.410256 0.809524
74 PLP CYS 0.4 0.873016
Ligand no: 2; Ligand: PLP; Similar ligands found: 62
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 F0G 0.564516 0.865385
12 MPM 0.564516 0.814815
13 FEV 0.555556 0.803571
14 KOU 0.555556 0.836364
15 HCP 0.546875 0.77193
16 EVM 0.546875 0.821429
17 6DF 0.545455 0.811321
18 PXL 0.541667 0.659574
19 Z98 0.537313 0.75
20 PXP 0.537037 0.862745
21 PMP 0.527273 0.767857
22 P0P 0.527273 0.916667
23 PL6 0.522388 0.818182
24 GT1 0.517857 0.830189
25 PFM 0.514706 0.803571
26 FEJ 0.514706 0.851852
27 LLP 0.5 0.737705
28 P70 0.5 0.833333
29 PUS 0.479452 0.707692
30 PL5 0.479452 0.775862
31 MPL 0.473684 0.836364
32 PLG 0.46875 0.75
33 IN5 0.46875 0.758621
34 P89 0.466667 0.714286
35 PLP PUT 0.463768 0.672131
36 EQJ 0.460526 0.725806
37 5DK 0.460526 0.725806
38 O1G 0.454545 0.75
39 PLT 0.439024 0.762712
40 X04 0.431034 0.851852
41 PDD 0.426471 0.762712
42 PP3 0.426471 0.762712
43 PDA 0.426471 0.762712
44 P1T 0.426471 0.714286
45 33P 0.42029 0.745763
46 IK2 0.42029 0.714286
47 TLP 0.414286 0.793103
48 2BK 0.414286 0.793103
49 PLS 0.414286 0.779661
50 2BO 0.414286 0.793103
51 5PA 0.414286 0.714286
52 PMH 0.414286 0.619718
53 9TD 0.413793 0.671642
54 PLP 999 0.410959 0.796296
55 PPD 0.408451 0.75
56 C6P 0.408451 0.75
57 QLP 0.405405 0.681818
58 MP5 0.403509 0.666667
59 PLA 0.402778 0.703125
60 PY5 0.402778 0.703125
61 HEY 0.4 0.703125
62 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 with APoc: 168
This union binding pocket(no: 1) in the query (biounit: 2wk9.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 4RKC PMP 1.02828
2 6C92 EQJ 1.06383
3 6C8T EQJ 1.06383
4 5VEQ PMP 1.79949
5 1DFO PLG 1.79949
6 1C7O PPG 1.79949
7 1B9I PXG 1.80412
8 5TH5 MET 1.90114
9 6CZY PMP 1.9337
10 5EYW PGA 2.00803
11 6CD1 PLS 2.05656
12 6CD1 PLG 2.05656
13 2HOX P1T 2.05656
14 1XI9 PLP 2.05656
15 4JE5 PLP 2.05656
16 4JE5 PMP 2.05656
17 2OGA PGU 2.05656
18 4OJP MAL 2.05656
19 2ZC0 PMP 2.31362
20 1PMO PLR 2.31362
21 2JFQ DGL 2.44755
22 3W5N RAM 2.57069
23 6CBN OZY 2.57069
24 1WD4 AHR 2.57069
25 3PD6 PMP 2.82776
26 3PDB PMP 2.82776
27 5G4J EXT 2.82776
28 3FQ8 PMP 2.82776
29 5U23 TQP 2.87958
30 4ZV1 ARG 3.00429
31 1K2V DEF 3.00752
32 3A8U PLP 3.08483
33 1GPM AMP 3.08483
34 2X5D PLP 3.08483
35 1JS3 PLP 142 3.08483
36 1M7Y PPG 3.08483
37 1LW4 PLP 3.17003
38 1LW4 TLP 3.17003
39 5IWQ PLP 3.3419
40 1B4N GUA 3.3419
41 2HHP FLC 3.3419
42 2FN1 SAL 3.3419
43 4JD0 1KH 3.58566
44 2ZX2 RAM 3.58974
45 4M2K PLP 3.59897
46 4FL0 PLP 3.59897
47 5WYF ILP 3.59897
48 2R5E QLP 3.59897
49 2R5C C6P 3.59897
50 3EI9 PL6 3.59897
51 5EQ8 HSO 3.61011
52 1LOP SIN ALA PRO ALA NIT 3.65854
53 1UGY GLA GLC 3.7594
54 5W70 9YM 3.82022
55 4IY7 0JO 3.85604
56 4IYO 0JO 3.85604
57 4IY7 KOU 3.85604
58 4ADC PLP 3.85604
59 4E1O PLP PVH 3.85604
60 2XCM ADP 4.05405
61 3LL9 ADP 4.08922
62 4BA5 PXG 4.11311
63 5DDW 5B6 4.11311
64 6EWR PMP 4.11311
65 4ZSY RW2 4.11311
66 1XT8 CYS 4.11311
67 1U08 PLP 4.14508
68 1LC8 33P 4.3956
69 5EXK MET 4.53172
70 6CBO DOW 4.55581
71 5W19 9TD 4.62725
72 5WXU FLC 4.62725
73 3ZRR PXG 4.6875
74 4AZJ SEP PLP 4.72222
75 1WYV PLP AOA 4.79452
76 4OX5 DAL 4.81283
77 4WXJ GLU 4.83271
78 6ECG PM9 4.88432
79 2TPL HPP 4.88432
80 5GVL PLG 4.88432
81 5GVL GI8 4.88432
82 5CMK LY5 5.01931
83 5M3Z PLP 5.14139
84 5M3Z PY6 5.14139
85 5M3Z NLE 5.14139
86 4UOX PLP 5.14139
87 4UOX PUT 5.14139
88 4UOX PLP PUT 5.14139
89 5KGS 6SR 5.14139
90 4A59 AMP 5.14139
91 4ZAH T5K 5.14139
92 5YSI NCA 5.26316
93 1CL2 PPG 5.39846
94 6DND PLP 5.39846
95 4ZM4 PLP 5.39846
96 4ZM4 P3B 5.39846
97 1AJS PLA 5.39846
98 3CQ5 PMP 5.42005
99 3HQ9 OXL 5.50725
100 1E5F PLP 5.65553
101 1SFF IK2 5.65553
102 2R2N PMP 5.9126
103 4K2M O1G 5.9126
104 6FYQ PLP 5.9126
105 1ZC9 PMP 5.9126
106 4R5Z PMP 5.99455
107 4R5Z SIN 5.99455
108 3SIX GDP 6.06061
109 3WGC PLG 6.15836
110 3BWN PMP 6.16967
111 3BWN PMP PHE 6.16967
112 2ZYJ PGU 6.16967
113 6C3C EJ1 6.16967
114 1IZO PAM 6.16967
115 1BCJ NGA 6.49351
116 3AB4 THR 6.74157
117 2RC8 DSN 6.80272
118 1PU7 39A 6.88073
119 4URS C2E 6.91489
120 4HVK PMP 7.06806
121 2X5F PLP 7.19794
122 4IO2 GLU 7.25806
123 6F5W KG1 7.31707
124 5W71 PLP 7.45501
125 1VJO PLP 7.45501
126 5W71 9YM 7.45501
127 4URG C2E 7.78443
128 5YKT PMP 7.96915
129 5K8B PDG 7.96915
130 6MFL OPV 8.11688
131 1GEX PLP HSA 8.14607
132 3WUR O4B 8.77193
133 4UHO PLP 8.99743
134 2FYF PLP 9.2545
135 2RCA GLY 9.58904
136 4IMO PWZ 9.65909
137 1SW1 PBE 9.81818
138 3VP6 HLD 10.0257
139 4E3Q PMP 10.2828
140 1H6H PIB 10.4895
141 1GDE GLU PLP 11.054
142 2PYY GLU 11.4035
143 4LNL PLG 12.012
144 4LNL 2BK 12.012
145 4LNL 2BO 12.012
146 1CZA G6P 12.3393
147 4AP9 1PS 12.4378
148 1UU1 PMP HSA 13.7313
149 3NUB UD0 14.2061
150 4WXG 2BO 14.2523
151 5G09 6DF 14.653
152 5X30 4LM 15.6812
153 5X30 7XF 15.6812
154 5X2Z 3LM 15.6812
155 4B98 PXG 16.1954
156 2OAT PFM 16.4524
157 2Z9V PXM 18.7661
158 4AOA IK2 18.7661
159 3BS8 PMP 18.7661
160 1M32 PLP 18.8525
161 4KQP GLN 22.4138
162 1GCK ASP PLP 22.5974
163 2O66 FLC 28.1481
164 1MLY ACZ PLP 29.3059
165 1FC4 AKB PLP 40.617
166 1DJ9 KAM 40.625
167 5TXR PLP 43.7018
168 2XBN PMP 43.9589
Pocket No.: 2; Query (leader) PDB : 2WK9; Ligand: PLG; Similar sites found with APoc: 184
This union binding pocket(no: 2) in the query (biounit: 2wk9.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
1 2NLQ GLY None
2 4RKC PMP 1.02828
3 6C92 EQJ 1.06383
4 6C8T EQJ 1.06383
5 5WS9 ATP 1.54242
6 3R4Z GLA 1.60428
7 1DFO PLG 1.79949
8 5VEQ PMP 1.79949
9 1C7O PPG 1.79949
10 1B9I PXG 1.80412
11 5TH5 MET 1.90114
12 6CZY PMP 1.9337
13 6CD1 PLS 2.05656
14 6CD1 PLG 2.05656
15 1XI9 PLP 2.05656
16 2HOX P1T 2.05656
17 4JE5 PLP 2.05656
18 4JE5 PMP 2.05656
19 2OGA PGU 2.05656
20 3P7I P7I 2.18069
21 2ZC0 PMP 2.31362
22 1PMO PLR 2.31362
23 3H2K BOG 2.31362
24 4HPP GLU 2.31362
25 2JFQ DGL 2.44755
26 6CBN OZY 2.57069
27 2CJH AKG 2.57069
28 1WD4 AHR 2.57069
29 2HJ9 AI2 2.65487
30 3PD6 PMP 2.82776
31 3PDB PMP 2.82776
32 5G4J EXT 2.82776
33 3FQ8 PMP 2.82776
34 4WCX MET 2.82776
35 5U23 TQP 2.87958
36 4ZV1 ARG 3.00429
37 1K2V DEF 3.00752
38 3PTG 932 3.0303
39 2X5D PLP 3.08483
40 3A8U PLP 3.08483
41 1GPM AMP 3.08483
42 1JS3 PLP 142 3.08483
43 1M7Y PPG 3.08483
44 1LW4 PLP 3.17003
45 1LW4 TLP 3.17003
46 5IWQ PLP 3.3419
47 2FN1 SAL 3.3419
48 2YJP CYS 3.43643
49 4M2K PLP 3.59897
50 5WYF ILP 3.59897
51 4FL0 PLP 3.59897
52 2R5C C6P 3.59897
53 2R5E QLP 3.59897
54 3EI9 PL6 3.59897
55 6GSZ BGC 3.59897
56 4NOS H4B 3.59897
57 5EQ8 HSO 3.61011
58 1LOP SIN ALA PRO ALA NIT 3.65854
59 1UGY GLA BGC 3.7594
60 1UGY GLA GLC 3.7594
61 5W70 9YM 3.82022
62 1DZT ATY 3.82514
63 4IY7 0JO 3.85604
64 4IYO 0JO 3.85604
65 4IY7 KOU 3.85604
66 4ADC PLP 3.85604
67 4E1O PLP PVH 3.85604
68 2XCM ADP 4.05405
69 3LL9 ADP 4.08922
70 4BA5 PXG 4.11311
71 5DDW 5B6 4.11311
72 6EWR PMP 4.11311
73 4ZSY RW2 4.11311
74 1XT8 CYS 4.11311
75 1RM8 BAT 4.14201
76 1U08 PLP 4.14508
77 1LC8 33P 4.3956
78 5EXK MET 4.53172
79 6CBO DOW 4.55581
80 5W19 9TD 4.62725
81 5WXU FLC 4.62725
82 3A9Y CYS 4.62725
83 3ZRR PXG 4.6875
84 4AZJ SEP PLP 4.72222
85 1WYV PLP AOA 4.79452
86 5WBF LAC 4.81482
87 4WXJ GLU 4.83271
88 6ECG PM9 4.88432
89 2TPL HPP 4.88432
90 5GVL GI8 4.88432
91 5GVL PLG 4.88432
92 5CMK LY5 5.01931
93 5M3Z PLP 5.14139
94 5M3Z PY6 5.14139
95 5M3Z NLE 5.14139
96 4UOX PLP 5.14139
97 4UOX PUT 5.14139
98 4UOX PLP PUT 5.14139
99 5KGS 6SR 5.14139
100 4ZAH T5K 5.14139
101 5YSI NCA 5.26316
102 1WDN GLN 5.30973
103 1CL2 PPG 5.39846
104 6DND PLP 5.39846
105 4ZM4 PLP 5.39846
106 4ZM4 P3B 5.39846
107 1AJS PLA 5.39846
108 3CQ5 PMP 5.42005
109 3HQ9 OXL 5.50725
110 1E5F PLP 5.65553
111 1SFF IK2 5.65553
112 4JH6 FCN 5.7971
113 2R2N PMP 5.9126
114 4K2M O1G 5.9126
115 6FYQ PLP 5.9126
116 1ZC9 PMP 5.9126
117 4R5Z PMP 5.99455
118 4R5Z SIN 5.99455
119 3WGC PLG 6.15836
120 3BWN PMP 6.16967
121 3BWN PMP PHE 6.16967
122 6C3C EJ1 6.16967
123 2ZYJ PGU 6.16967
124 1IZO PAM 6.16967
125 5HVJ ANP 6.34921
126 1II5 GLU 6.43777
127 1BCJ NGA 6.49351
128 2RC8 DSN 6.80272
129 1PU7 39A 6.88073
130 4HVK PMP 7.06806
131 2X5F PLP 7.19794
132 6EV2 BGC 7.20721
133 4IO2 GLU 7.25806
134 5W71 PLP 7.45501
135 1VJO PLP 7.45501
136 5W71 9YM 7.45501
137 4CU1 H4B 7.71208
138 5YKT PMP 7.96915
139 5K8B PDG 7.96915
140 6MFL OPV 8.11688
141 1GEX PLP HSA 8.14607
142 3SXS PP2 8.58209
143 4UHO PLP 8.99743
144 1ELU PDA 8.99743
145 2FYF PLP 9.2545
146 2UVO NDG 9.35672
147 4AML GYU 9.35672
148 2HUI GLV 9.51157
149 2RCA GLY 9.58904
150 1SW1 PBE 9.81818
151 3VP6 HLD 10.0257
152 4E3Q PMP 10.2828
153 1GDE GLU PLP 11.054
154 4LNL PLG 12.012
155 4LNL 2BK 12.012
156 4LNL 2BO 12.012
157 1CZA G6P 12.3393
158 1OD3 BGC BGC 13.0952
159 1UU1 PMP HSA 13.7313
160 3NUB UD0 14.2061
161 4WXG 2BO 14.2523
162 5G09 6DF 14.653
163 3KYF 5GP 5GP 14.7186
164 5X30 4LM 15.6812
165 5X30 7XF 15.6812
166 5X2Z 3LM 15.6812
167 1K7U NAG NAG 16.129
168 1K7V NAG GAL BGC 16.129
169 4B98 PXG 16.1954
170 2OAT PFM 16.4524
171 4YSX MLI 18.5897
172 2Z9V PXM 18.7661
173 4AOA IK2 18.7661
174 3BS8 PMP 18.7661
175 1M32 PLP 18.8525
176 4KQP GLN 22.4138
177 1GCK ASP PLP 22.5974
178 1SQL GUN 23.9726
179 2O66 FLC 28.1481
180 1MLY ACZ PLP 29.3059
181 1FC4 AKB PLP 40.617
182 1DJ9 KAM 40.625
183 5TXR PLP 43.7018
184 2XBN PMP 43.9589
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