Receptor
PDB id Resolution Class Description Source Keywords
2C42 1.78 Å EC: 1.2.7.1 CRYSTAL STRUCTURE OF PYRUVATE-FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS DESULFOVIBRIO AFRICANUS OXIDOREDUCTASE 4FE-4S IRON IRON-SULFUR IRON-SULFUR CLUSTER PYRUVATE CATABOLISM TPP-DEPENDENT ENZYME METAL-BINDING ELECTRON TRANSPORT
Ref.: FLEXIBILITY OF THIAMINE DIPHOSPHATE REVEALED BY KINETIC CRYSTALLOGRAPHIC STUDIES OF THE REACTION OF PYRUVATE-FERREDOXIN OXIDOREDUCTASE WITH PYRUVATE. STRUCTURE V. 14 217 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:3239;
B:3239;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
MG A:3238;
B:3238;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
PYR A:3237;
B:3237;
Valid;
Valid;
none;
none;
submit data
88.062 C3 H4 O3 CC(=O...
SF4 A:3233;
A:3234;
A:3235;
B:3233;
B:3234;
B:3235;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
submit data
351.64 Fe4 S4 [S]12...
TPP A:3236;
B:3236;
Valid;
Valid;
none;
none;
submit data
425.314 C12 H19 N4 O7 P2 S Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2C42 1.78 Å EC: 1.2.7.1 CRYSTAL STRUCTURE OF PYRUVATE-FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS DESULFOVIBRIO AFRICANUS OXIDOREDUCTASE 4FE-4S IRON IRON-SULFUR IRON-SULFUR CLUSTER PYRUVATE CATABOLISM TPP-DEPENDENT ENZYME METAL-BINDING ELECTRON TRANSPORT
Ref.: FLEXIBILITY OF THIAMINE DIPHOSPHATE REVEALED BY KINETIC CRYSTALLOGRAPHIC STUDIES OF THE REACTION OF PYRUVATE-FERREDOXIN OXIDOREDUCTASE WITH PYRUVATE. STRUCTURE V. 14 217 2006
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2C3U - PYR C3 H4 O3 CC(=O)C(=O....
2 2C42 - PYR C3 H4 O3 CC(=O)C(=O....
3 1B0P - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
4 2C3M - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
5 1KEK - HTL C14 H21 N4 O8 P2 S Cc1c(sc([n....
6 2C3Y - HTL C14 H21 N4 O8 P2 S Cc1c(sc([n....
7 2C3P - 1TP C15 H26 N4 O10 P2 S Cc1ncc(c(n....
8 2UZA - HTL C14 H21 N4 O8 P2 S Cc1c(sc([n....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2C3U - PYR C3 H4 O3 CC(=O)C(=O....
2 2C42 - PYR C3 H4 O3 CC(=O)C(=O....
3 1B0P - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
4 2C3M - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
5 1KEK - HTL C14 H21 N4 O8 P2 S Cc1c(sc([n....
6 2C3Y - HTL C14 H21 N4 O8 P2 S Cc1c(sc([n....
7 2C3P - 1TP C15 H26 N4 O10 P2 S Cc1ncc(c(n....
8 2UZA - HTL C14 H21 N4 O8 P2 S Cc1c(sc([n....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2C3U - PYR C3 H4 O3 CC(=O)C(=O....
2 2C42 - PYR C3 H4 O3 CC(=O)C(=O....
3 1B0P - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
4 2C3M - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
5 1KEK - HTL C14 H21 N4 O8 P2 S Cc1c(sc([n....
6 2C3Y - HTL C14 H21 N4 O8 P2 S Cc1c(sc([n....
7 2C3P - 1TP C15 H26 N4 O10 P2 S Cc1ncc(c(n....
8 2UZA - HTL C14 H21 N4 O8 P2 S Cc1c(sc([n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PYR; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 PYR 1 1
2 ACY 0.636364 0.636364
3 OXD 0.545455 0.642857
4 KIV 0.411765 0.785714
5 AAE 0.411765 0.625
6 2KT 0.411765 0.733333
Ligand no: 2; Ligand: TPP; Similar ligands found: 41
No: Ligand ECFP6 Tc MDL keys Tc
1 TPP 1 1
2 V4E 0.891892 1
3 TDP 0.84 0.985714
4 TPS 0.816901 0.957143
5 TMV 0.769231 0.958333
6 2TP 0.725 0.932432
7 VNP 0.721519 0.958904
8 VIB 0.621622 0.75
9 PYI 0.581395 0.887324
10 TDW 0.566667 0.972222
11 HTL 0.566667 0.958904
12 N1T 0.556818 0.985714
13 FTP 0.551724 0.835616
14 THV 0.548387 0.958904
15 TPW 0.546512 0.9
16 WWF 0.542553 0.933333
17 TD6 0.540816 0.921053
18 THY 0.536842 0.945946
19 TOG 0.536082 0.921053
20 TDL 0.53125 0.897436
21 THW 0.530612 0.958904
22 TD9 0.53 0.921053
23 TD8 0.53 0.921053
24 TDK 0.525773 0.921053
25 D7K 0.490566 0.909091
26 S1T 0.489362 0.887324
27 R1T 0.489362 0.887324
28 TPU 0.483146 0.842105
29 5SR 0.479167 0.945205
30 T5X 0.476636 0.897436
31 T6F 0.476636 0.897436
32 1U0 0.474227 0.84
33 8PA 0.459459 0.945946
34 TZD 0.451613 0.883117
35 O2T 0.45098 0.909091
36 TDM 0.443299 0.894737
37 TDN 0.415842 0.871795
38 THD 0.411765 0.839506
39 MP5 0.407895 0.676056
40 TD7 0.40566 0.85
41 DPX 0.4 0.734177
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2C42; Ligand: PYR; Similar sites found: 113
This union binding pocket(no: 1) in the query (biounit: 2c42.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1RP7 TZD 0.003764 0.40614 1.24153
2 3Q3H UDP 0.01974 0.42041 1.26783
3 3OTH TYD 0.01389 0.40876 1.29976
4 2O1S TDP 0.008527 0.41879 1.44928
5 2OVW CBI 0.03643 0.4022 1.45985
6 4I3G BGC 0.03259 0.40474 1.68878
7 2CYB TYR 0.01832 0.42271 1.85759
8 2X7J TPP 0.00001641 0.50405 1.8684
9 5ESO TDP 0.000009062 0.47493 1.91638
10 5ESO ISC 0.000009062 0.47493 1.91638
11 1DAR GDP 0.02831 0.40415 2.02605
12 1V5F FAD 0.002125 0.43763 2.03735
13 1T9D P22 0.000003451 0.61977 2.06795
14 1T9D PYD 0.0000671 0.53016 2.06795
15 1PIE GLA 0.03899 0.40488 2.14797
16 2VF7 ADP 0.02071 0.40735 2.25653
17 5DNC ASN 0.02496 0.41081 2.27457
18 2O7B HC4 0.01945 0.40516 2.30326
19 1K6M AGS 0.01028 0.40206 2.31481
20 4JBL MET 0.04538 0.40094 2.35988
21 3IAE D7K 0.0000007055 0.53165 2.45614
22 2UZ1 TPP 0.0000004467 0.56711 2.48668
23 2IYA UDP 0.01737 0.40091 2.59434
24 2NXW TPP 0.0000002724 0.53531 2.65487
25 1QS0 TDP 0.009204 0.4072 2.7027
26 3S2U UD1 0.01096 0.40085 2.73973
27 2Z9I GLY ALA THR VAL 0.03777 0.40765 2.77778
28 2R68 SUP 0.03451 0.40737 2.80561
29 1QPB PYM 0.00000006888 0.59374 2.84192
30 1QPB TPP 0.00000007786 0.59163 2.84192
31 4R8L ASP 0.01575 0.42124 2.85714
32 1ZUW DGL 0.03448 0.40345 2.94118
33 1FNZ A2G 0.0217 0.42108 2.95359
34 1ZPD DPX 0.0000002386 0.56154 2.99296
35 4ZOW CLM 0.008166 0.40951 3.06905
36 2IYF UDP 0.01772 0.40373 3.13253
37 3CL5 SIO 0.01213 0.43392 3.18302
38 2GPT TLA 0.02434 0.41654 3.25048
39 3U6K GDP 0.02393 0.40788 3.29949
40 4X1Z FUC GAL NDG 0.01842 0.42087 3.31325
41 4O48 ASP 0.04199 0.40434 3.31325
42 3HQP OXL 0.02735 0.41674 3.40681
43 4PPF FLC 0.04245 0.4071 3.42857
44 2AK3 AMP 0.04316 0.40142 3.53982
45 1KC7 PPR 0.0217 0.42323 3.55097
46 4RLQ 3SK 0.01171 0.43252 3.66089
47 4E28 9MZ 0.03145 0.40563 3.69231
48 3CQL NDG 0.03582 0.40743 3.7037
49 2AJ4 GLA 0.02045 0.41958 3.83212
50 4BQS K2Q 0.02716 0.40889 3.97727
51 3AI7 TPP 0.001902 0.42086 4.21179
52 2ACV UDP 0.02083 0.40372 4.31965
53 1YBH P22 0.000002199 0.61166 4.40678
54 1P4V GLY 0.02309 0.41887 4.40678
55 4NZ6 DLY 0.04457 0.40022 4.47284
56 1UPA TPP 0.0000009623 0.55368 4.53752
57 2IHT TPP 0.000001734 0.54338 4.53752
58 2IHU TP9 0.000001664 0.49491 4.53752
59 3EYA TDP 0.0000004958 0.56529 4.55373
60 2VBF TPP 0.0000003478 0.55528 4.5614
61 2Z49 AMG 0.01522 0.41313 4.62963
62 1HQL GLA MBG 0.0439 0.40862 4.66926
63 3AI8 HNQ 0.04329 0.40205 4.6875
64 2XDQ MGX 0.009206 0.42654 4.69667
65 1UMD TDP COI 0.0007445 0.43729 4.90463
66 4WBD CIT 0.04041 0.41237 5.36044
67 2CHT TSA 0.04256 0.40245 5.51181
68 1KSK URA 0.01649 0.43296 5.55556
69 1XKV ATP 0.02416 0.40058 5.67108
70 1YRB GDP 0.01999 0.40124 5.72519
71 1YQT ADP 0.01408 0.42827 5.76208
72 1W55 GPP 0.02646 0.44833 5.92992
73 2JFN GLU 0.02974 0.40305 5.96491
74 1FWV SGA MAG FUC 0.0409 0.40451 5.97015
75 3LE7 ADE 0.01117 0.43338 6.13027
76 2VK4 TPP 0.00000006984 0.59959 6.2167
77 4RDN 6MD 0.01593 0.42679 6.58683
78 3NCQ ATP 0.003231 0.42395 6.72269
79 2X7I CIT 0.009544 0.42816 6.81818
80 1IZC PYR 0.01249 0.41845 7.07965
81 2UZH IPE 0.02916 0.41365 7.27273
82 1KJ1 MAN 0.02814 0.40633 7.33945
83 3FSJ D7K 0.0005042 0.4217 7.38636
84 3WCS MAN NAG GAL 0.01975 0.41213 7.48031
85 3WCS MAN NAG 0.04203 0.40274 7.48031
86 4U36 TNR 0.04955 0.40018 7.5
87 4CUB GAL NAG 0.03662 0.40425 8.19672
88 4USI ATP 0.01104 0.40071 8.44156
89 2OZL TPP 0.001423 0.43942 8.79765
90 3EXH TPP 0.001048 0.44519 9.11854
91 1FHW I5P 0.0376 0.40642 9.30233
92 2AWN ADP 0.03234 0.4038 9.44882
93 1OJJ GLC GAL 0.02498 0.41079 10.199
94 5T96 79J 0.03283 0.4111 10.2339
95 3DVA TPW 0.002438 0.41651 10.4615
96 4RJK TPP 0.0000003616 0.55984 10.683
97 4RJK TDL 0.0000003246 0.55136 10.683
98 2PUZ NIG 0.04658 0.40032 10.7399
99 1V3S ATP 0.005014 0.41891 11.2069
100 4G28 0W8 0.01388 0.42411 11.4094
101 1M7G AV2 0.01134 0.42867 13.2701
102 1H4H XYP XYS XYP 0.01738 0.40413 13.8756
103 1VKF CIT 0.03697 0.40285 14.3617
104 1FWY UD1 0.01272 0.40095 14.8036
105 4E03 ADP 0.03226 0.40497 16.0194
106 5B48 TDN 0.00000000005193 0.69417 16.0656
107 1W85 TDP 0.002303 0.43034 16.3265
108 1LYX PGA 0.01549 0.40996 16.9355
109 5DQY BEZ 0.04209 0.40457 17.1429
110 2J9D ADP 0.001822 0.43126 19.3277
111 2J9D AMP 0.007857 0.41689 19.3277
112 2QQC AG2 0.02059 0.41943 26.4151
113 5EXE 5SR 0.000000000004856 0.73289 35.443
Pocket No.: 2; Query (leader) PDB : 2C42; Ligand: PYR; 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: 2c42.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2C42; Ligand: TPP; Similar sites found: 58
This union binding pocket(no: 3) in the query (biounit: 2c42.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1RP7 TZD 0.003764 0.40614 1.24153
2 3Q3H UDP 0.01974 0.42041 1.26783
3 4I3G BGC 0.03259 0.40474 1.68878
4 2CYB TYR 0.01832 0.42271 1.85759
5 2X7J TPP 0.00001641 0.50405 1.8684
6 5ESO TDP 0.000009062 0.47493 1.91638
7 5ESO ISC 0.000009062 0.47493 1.91638
8 1DAR GDP 0.02831 0.40415 2.02605
9 1T9D P22 0.000003451 0.61977 2.06795
10 1T9D PYD 0.0000671 0.53016 2.06795
11 1PIE GLA 0.03899 0.40488 2.14797
12 2VF7 ADP 0.02071 0.40735 2.25653
13 5DNC ASN 0.02496 0.41081 2.27457
14 2O7B HC4 0.01945 0.40516 2.30326
15 4JBL MET 0.04538 0.40094 2.35988
16 2UZ1 TPP 0.0000004467 0.56711 2.48668
17 2NXW TPP 0.0000002724 0.53531 2.65487
18 1QPB PYM 0.00000006888 0.59374 2.84192
19 1QPB TPP 0.00000007786 0.59163 2.84192
20 4R8L ASP 0.01575 0.42124 2.85714
21 1ZPD DPX 0.0000002386 0.55189 2.99296
22 4ZOW CLM 0.008166 0.40951 3.06905
23 4X1Z FUC GAL NDG 0.01842 0.42087 3.31325
24 3HQP OXL 0.02735 0.41674 3.40681
25 4PPF FLC 0.04245 0.4071 3.42857
26 4RLQ 3SK 0.01171 0.43252 3.66089
27 3AI7 TPP 0.001902 0.42086 4.21179
28 2ACV UDP 0.02083 0.40372 4.31965
29 1P4V GLY 0.02309 0.41887 4.40678
30 4NZ6 DLY 0.04457 0.40022 4.47284
31 1UPA TPP 0.0000009623 0.55368 4.53752
32 2IHU TP9 0.000001664 0.53377 4.53752
33 2IHT TPP 0.000001734 0.5068 4.53752
34 3EYA TDP 0.0000004958 0.56529 4.55373
35 2VBF TPP 0.0000003478 0.54568 4.5614
36 2Z49 AMG 0.01522 0.41313 4.62963
37 1UMD TDP COI 0.0007445 0.43729 4.90463
38 2CHT TSA 0.04256 0.40245 5.51181
39 1XKV ATP 0.02416 0.40058 5.67108
40 1YQT ADP 0.01408 0.42827 5.76208
41 1FWV SGA MAG FUC 0.0409 0.40451 5.97015
42 2VK4 TPP 0.00000006984 0.59959 6.2167
43 4RDN 6MD 0.01593 0.42679 6.58683
44 1KJ1 MAN 0.02814 0.40633 7.33945
45 4CUB GAL NAG 0.03662 0.40425 8.19672
46 4USI ATP 0.01104 0.40071 8.44156
47 3EXH TPP 0.001048 0.44519 9.11854
48 1OJJ GLC GAL 0.02498 0.41079 10.199
49 5T96 79J 0.03283 0.4111 10.2339
50 3DVA TPW 0.002438 0.41651 10.4615
51 4RJK TPP 0.0000002839 0.56393 10.683
52 2PUZ NIG 0.04658 0.40032 10.7399
53 1H4H XYP XYS XYP 0.01738 0.40413 13.8756
54 5B48 TDN 0.00000000005193 0.69417 16.0656
55 5DQY BEZ 0.04209 0.40457 17.1429
56 2J9D ADP 0.001822 0.43126 19.3277
57 2J9D AMP 0.007857 0.41689 19.3277
58 5EXE 5SR 0.000000000004856 0.73289 35.443
Pocket No.: 4; Query (leader) PDB : 2C42; Ligand: TPP; 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: 2c42.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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