Receptor
PDB id Resolution Class Description Source Keywords
1ZPD 1.86 Å EC: 4.1.1.1 PYRUVATE DECARBOXYLASE FROM ZYMOMONAS MOBILIS ZYMOMONAS MOBILIS ALCOHOL FERMENTATION THIAMIN DIPHOSPHATE DECARBOXYLASE
Ref.: HIGH RESOLUTION CRYSTAL STRUCTURE OF PYRUVATE DECARBOXYLASE FROM ZYMOMONAS MOBILIS. IMPLICATIONS FOR SUBSTRATE ACTIVATION IN PYRUVATE DECARBOXYLASES. J.BIOL.CHEM. V. 273 20196 1998
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CIT A:610;
B:610;
E:610;
F:610;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
192.124 C6 H8 O7 C(C(=...
DPX A:600;
B:600;
E:600;
F:600;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
430.311 C11 H20 N4 O8 P2 S Cc1nc...
MG A:601;
B:601;
E:601;
F:601;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1ZPD 1.86 Å EC: 4.1.1.1 PYRUVATE DECARBOXYLASE FROM ZYMOMONAS MOBILIS ZYMOMONAS MOBILIS ALCOHOL FERMENTATION THIAMIN DIPHOSPHATE DECARBOXYLASE
Ref.: HIGH RESOLUTION CRYSTAL STRUCTURE OF PYRUVATE DECARBOXYLASE FROM ZYMOMONAS MOBILIS. IMPLICATIONS FOR SUBSTRATE ACTIVATION IN PYRUVATE DECARBOXYLASES. J.BIOL.CHEM. V. 273 20196 1998
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2WVG - TPU C11 H18 N6 O7 P2 Cc1c(nnn1C....
2 3OE1 - TDL C15 H23 N4 O10 P2 S Cc1c(sc([n....
3 2WVA - PYR C3 H4 O3 CC(=O)C(=O....
4 1ZPD - DPX C11 H20 N4 O8 P2 S Cc1ncc(c(n....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2WVG - TPU C11 H18 N6 O7 P2 Cc1c(nnn1C....
2 3OE1 - TDL C15 H23 N4 O10 P2 S Cc1c(sc([n....
3 2WVA - PYR C3 H4 O3 CC(=O)C(=O....
4 1ZPD - DPX C11 H20 N4 O8 P2 S Cc1ncc(c(n....
50% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2VK8 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 1PYD - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
3 1QPB Kd = 44 mM PYM C3 H5 N O2 CC(=O)C(=O....
4 2VK1 - TPP PYR n/a n/a
5 1PVD - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
6 2VBG - R1T C15 H23 N3 O8 P2 S Cc1c(sc(c1....
7 2VBF - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
8 2VK4 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
9 2VJY - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
10 2WVG - TPU C11 H18 N6 O7 P2 Cc1c(nnn1C....
11 3OE1 - TDL C15 H23 N4 O10 P2 S Cc1c(sc([n....
12 2WVA - PYR C3 H4 O3 CC(=O)C(=O....
13 1ZPD - DPX C11 H20 N4 O8 P2 S Cc1ncc(c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CIT; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 CIT 1 1
2 HCA 0.576923 0.884615
3 MAH 0.44 0.807692
Ligand no: 2; Ligand: DPX; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 DPX 1 1
2 TP9 0.517241 0.9
3 PYI 0.430108 0.746667
4 MP5 0.424658 0.705882
5 TPU 0.417582 0.7125
6 TPP 0.4 0.734177
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1ZPD; Ligand: CIT; Similar sites found: 65
This union binding pocket(no: 1) in the query (biounit: 1zpd.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3NT6 COA 0.04022 0.40486 1.58451
2 3NTD COA 0.04064 0.40843 1.59292
3 4U0S ADP 0.02155 0.40309 1.74419
4 2Q2Y MKR 0.03929 0.41567 2.11268
5 2Q2Y ADP 0.04071 0.41567 2.11268
6 4RHP PEF 0.0182 0.41706 2.12766
7 4QEK GLC 0.01306 0.40205 2.65781
8 2UW1 GVM 0.01172 0.40664 2.66272
9 2JC9 ADN 0.01322 0.4071 2.7027
10 2OWZ CIT 0.01045 0.40476 2.71084
11 4LSJ LSJ 0.02145 0.41419 2.71318
12 3QP8 HL0 0.01796 0.41193 2.71739
13 2Q1H AS4 0.02434 0.41036 2.8
14 1H9G COA MYR 0.01097 0.4255 2.88066
15 5V3Y 5V8 0.01552 0.41313 3.14685
16 2E2R 2OH 0.04776 0.40792 3.27869
17 2I0G I0G 0.02282 0.43693 3.50195
18 1U25 IHS 0.001266 0.44881 3.56083
19 1SR7 MOF 0.02186 0.42687 3.87324
20 3SVJ 4LI 0.0067 0.43792 3.94089
21 1NTV ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 0.01766 0.42183 3.94737
22 1FM9 9CR 0.01882 0.42238 4.04412
23 1FM9 570 0.03531 0.40933 4.04412
24 3G9E RO7 0.01522 0.4277 4.05904
25 5N7O 69Y 0.01311 0.41045 4.0724
26 3M6P BB2 0.02689 0.40005 4.14508
27 2RH1 CAU 0.01711 0.4078 4.22535
28 3G4G D71 0.02033 0.41358 4.27553
29 2C43 COA 0.01964 0.41734 4.33437
30 3BQ5 HCS 0.04246 0.40646 4.40141
31 1YMT DR9 0.04776 0.40524 4.87805
32 3B9Z CO2 0.02061 0.40162 4.89691
33 4WH9 3M8 0.0009829 0.45155 4.91803
34 5V4R MGT 0.005973 0.42065 4.93827
35 2VWA PTY 0.0082 0.40885 4.9505
36 2VAT COA 0.01954 0.41736 4.95496
37 1GHE ACO 0.0189 0.41612 5.08475
38 5V13 JH3 0.0009729 0.48249 5.20833
39 2Q0D ATP 0.02006 0.43015 5.38244
40 2QZT PLM 0.02879 0.40964 5.40541
41 2O1V ADP 0.01852 0.40602 5.6338
42 4ZGM 32M 0.00461 0.42824 5.7377
43 4RW3 TDA 0.00648 0.42869 5.96026
44 4RW3 PLM 0.007121 0.42334 5.96026
45 3BQD DAY 0.01865 0.41922 6.27451
46 4P6X HCY 0.01923 0.41321 6.27451
47 1ATL 0QI 0.02776 0.40942 6.43564
48 3EE4 MYR 0.008415 0.43282 6.50155
49 2BIF BOG 0.006912 0.44026 6.82303
50 3WCA FPS 0.04058 0.40818 6.84932
51 1YBU APC 0.02506 0.40155 7.06522
52 1VG0 GER 0.01549 0.41013 7.24638
53 5XNA SHV 0.0102 0.40471 7.24638
54 3ZQE DXC 0.005712 0.41724 7.86885
55 3KDU NKS 0.0225 0.4306 7.94224
56 4K90 MLA 0.01053 0.40233 8.83721
57 4TMK T5A 0.03718 0.41117 8.92019
58 3HY9 098 0.03037 0.40171 9.95475
59 3PMD 11A 0.011 0.41723 10.4575
60 5OCA 9QZ 0.0117 0.41025 10.5042
61 5TVI MYR 0.001415 0.46463 10.8696
62 5C1M 4VO 0.006998 0.42449 12
63 5C1M CLR 0.0123 0.41205 12
64 3N7S 3N7 0.004927 0.42567 12.1739
65 3JRS A8S 0.01828 0.41187 12.5
Pocket No.: 2; Query (leader) PDB : 1ZPD; Ligand: DPX; 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: 1zpd.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1ZPD; Ligand: DPX; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 1zpd.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1ZPD; Ligand: CIT; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 1zpd.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1ZPD; Ligand: DPX; Similar sites found: 101
This union binding pocket(no: 5) in the query (biounit: 1zpd.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5A3Y VAL LYS 0.03854 0.40445 1.09489
2 5ESO TDP 0.000000008068 0.57341 1.23239
3 5ESO ISC 0.000000008068 0.57341 1.23239
4 2ACV UDP 0.003809 0.43805 1.2959
5 2H92 C5P 0.01044 0.41699 1.36986
6 1R9J TPP 0.000311 0.45845 1.58451
7 2VF7 ADP 0.02689 0.4005 1.76056
8 2J5V PCA 0.02494 0.41964 1.90736
9 1RRV TYD 0.01713 0.40319 1.92308
10 5T96 79J 0.04259 0.4017 2.04678
11 1KSK URA 0.007474 0.45068 2.13675
12 3CTL S6P 0.0127 0.40277 2.1645
13 3PNQ 2HA 0.0153 0.41822 2.2409
14 5XDR ADP 0.02407 0.40289 2.28873
15 1H5R G1P 0.02173 0.40509 2.38908
16 2IYA UDP 0.006399 0.4197 2.59434
17 1YQT ADP 0.04507 0.40125 2.60223
18 5ND5 TPP 0.0003888 0.45441 2.64085
19 3OTH TYD 0.0134 0.40823 2.6699
20 4A1O JLN 0.005827 0.40546 2.67686
21 2ZWI C5P 0.02949 0.40205 2.68097
22 2DPY ADP 0.02161 0.41708 2.96804
23 2C42 PYR 0.0000002386 0.56154 2.99296
24 2C42 TPP 0.0000002386 0.55189 2.99296
25 3OID TCL 0.04495 0.4 3.10078
26 5B48 TDN 0.0000001368 0.5606 3.27869
27 4U00 ADP 0.02044 0.41557 3.27869
28 3RK0 AMP 0.01325 0.41572 3.37553
29 4UP4 NAG 0.01222 0.42224 3.49127
30 4UP4 NDG 0.01222 0.42224 3.49127
31 5EVY FAD 0.005514 0.40646 3.65297
32 1ITZ TPP 0.0003624 0.45568 3.69718
33 5TPC GAL SIA NGA GAL SIA 0.01118 0.43797 3.76471
34 5DQY BEZ 0.02635 0.41062 3.80952
35 3W9F I3P 0.009814 0.46173 3.84615
36 4PPF FLC 0.03988 0.41149 4
37 2BDG PBZ 0.02288 0.41575 4.03587
38 2YIC TPP 0.0009755 0.42484 4.0493
39 2OG2 MLI 0.007422 0.41938 4.0493
40 3ITJ CIT 0.02807 0.41236 4.14201
41 4D52 GXL 0.03188 0.40393 4.22535
42 5JDI 6JO 0.0273 0.41333 4.51389
43 2R5N R5P 0.000859 0.40826 4.57746
44 2R5N TPP 0.001061 0.40499 4.57746
45 2R5N RP5 0.000934 0.40364 4.57746
46 1UMD TDP COI 0.0001828 0.46025 4.62963
47 1WYV PLP AOA 0.01766 0.40257 4.64135
48 3HWW AKG 0.00007729 0.51338 4.67626
49 3EXH TPP 0.0003877 0.46238 4.71204
50 3HY2 ATP 0.02576 0.40889 4.85437
51 2OZL TPP 0.0003653 0.4635 4.93151
52 1EC9 XYH 0.006759 0.4186 4.93274
53 3AI7 TPP 0.00008019 0.4746 5.10563
54 1RP7 TZD 0.000879 0.42969 5.10563
55 1UPA TPP 0.00000002566 0.61477 5.28169
56 2IHT TPP 0.00000004634 0.56903 5.28169
57 5M0T AKG 0.03696 0.40434 5.44218
58 2IHU TP9 0.00000001147 0.56216 5.45775
59 1V5F FAD 0.0001062 0.49527 5.45775
60 4CCO OGA 0.04201 0.40159 5.56745
61 2QV7 ADP 0.01972 0.40029 5.63798
62 3B5J 12D 0.01457 0.4262 5.76132
63 5EXE 5SR 0.000001444 0.52285 6.03175
64 1G8S MET 0.02203 0.41653 6.08696
65 4XDA RIB 0.02622 0.40465 6.14887
66 3DVA TPW 0.001316 0.42586 6.15385
67 2O66 FLC 0.02393 0.41637 6.66667
68 1JI0 ATP 0.02552 0.41321 6.66667
69 5TG5 JW8 0.04165 0.40381 6.93878
70 5FJJ MAN 0.005031 0.42291 7.21831
71 3B9Q MLI 0.01675 0.40871 7.61589
72 2O1S TDP 0.0001014 0.50786 7.74648
73 1GXS DKA 0.0442 0.40222 8.22785
74 4NV0 MG7 0.04387 0.40057 8.46395
75 4JEJ 1GP 0.01712 0.41022 9.01639
76 1G6H ADP 0.03238 0.40553 9.72763
77 1W85 TDP 0.001424 0.43796 10.2041
78 2X7J TPP 0.00000003526 0.60923 10.5634
79 3P13 RIP 0.0147 0.41304 11.1111
80 2Y5S 78H 0.02221 0.40462 11.5646
81 5EOO CIT 0.04447 0.40152 13.2075
82 1OZH HE3 0.0000001863 0.43861 14.6643
83 4RJK TDL 0.000000004928 0.61456 15.1408
84 4RJK TPP 0.000000015 0.61123 15.1408
85 3IT6 ORN 0.03992 0.40466 16.5854
86 2QQC AG2 0.0312 0.40854 22.3214
87 4WZ6 ATP 0.02321 0.41761 22.4138
88 2C31 TZD 0.0000006093 0.59675 34.1549
89 2C31 ADP 0.000000583 0.59665 34.1549
90 2Q28 TPP 0.00001393 0.50509 35.5634
91 3FSJ D7K 0.000002873 0.49643 38.3803
92 2UZ1 TPP 0.0000000002034 0.69903 38.7324
93 3IAE D7K 0.0000000005107 0.6403 38.7324
94 1T9D P22 0.00000003016 0.72653 41.0211
95 1YBH P22 0.00000006616 0.68611 41.0211
96 1T9D PYD 0.0000001085 0.6654 41.0211
97 1T9D P25 0.00000000221 0.4147 41.0211
98 1T9D FAD 0.000000002616 0.41329 41.0211
99 1T9D 1MM 0.000000002759 0.4106 41.0211
100 3EYA TDP 0.00000000277 0.65354 41.9014
101 2NXW TPP 0.0000000000613 0.66374 44.4248
Pocket No.: 6; Query (leader) PDB : 1ZPD; Ligand: CIT; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 1zpd.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 1ZPD; Ligand: DPX; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 1zpd.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 1ZPD; Ligand: CIT; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 1zpd.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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