Receptor
PDB id Resolution Class Description Source Keywords
1B0P 2.31 Å EC: 1.2.7.1 CRYSTAL STRUCTURE OF PYRUVATE-FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS DESULFOVIBRIO AFRICANUS OXIDOREDUCTASE PYRUVATE CATABOLISM IRON-SULFUR CLUSTER TPDEPENDENT ENZYME
Ref.: CRYSTAL STRUCTURES OF THE KEY ANAEROBIC ENZYME PYRUVATE:FERREDOXIN OXIDOREDUCTASE, FREE AND IN COM PYRUVATE. NAT.STRUCT.BIOL. V. 6 182 1999
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:1238;
B:1238;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
MG A:1237;
B:1237;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
SF4 A:1233;
A:1234;
A:1235;
B:1233;
B:1234;
B:1235;
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:1236;
B:1236;
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 1B0P - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 2C3M - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
3 1KEK - HTL C14 H21 N4 O8 P2 S Cc1c(sc([n....
4 2C3Y - HTL C14 H21 N4 O8 P2 S Cc1c(sc([n....
5 2C3P - 1TP C15 H26 N4 O10 P2 S Cc1ncc(c(n....
6 2C3U - PYR C3 H4 O3 CC(=O)C(=O....
7 2UZA - HTL C14 H21 N4 O8 P2 S Cc1c(sc([n....
8 2C42 - PYR C3 H4 O3 CC(=O)C(=O....
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 1B0P - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 2C3M - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
3 1KEK - HTL C14 H21 N4 O8 P2 S Cc1c(sc([n....
4 2C3Y - HTL C14 H21 N4 O8 P2 S Cc1c(sc([n....
5 2C3P - 1TP C15 H26 N4 O10 P2 S Cc1ncc(c(n....
6 2C3U - PYR C3 H4 O3 CC(=O)C(=O....
7 2UZA - HTL C14 H21 N4 O8 P2 S Cc1c(sc([n....
8 2C42 - PYR C3 H4 O3 CC(=O)C(=O....
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 1B0P - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 2C3M - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
3 1KEK - HTL C14 H21 N4 O8 P2 S Cc1c(sc([n....
4 2C3Y - HTL C14 H21 N4 O8 P2 S Cc1c(sc([n....
5 2C3P - 1TP C15 H26 N4 O10 P2 S Cc1ncc(c(n....
6 2C3U - PYR C3 H4 O3 CC(=O)C(=O....
7 2UZA - HTL C14 H21 N4 O8 P2 S Cc1c(sc([n....
8 2C42 - PYR C3 H4 O3 CC(=O)C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TPP; Similar ligands found: 36
No: Ligand ECFP6 Tc MDL keys Tc
1 TPP 1 1
2 TDP 0.84 0.985714
3 TPS 0.816901 0.957143
4 TMV 0.769231 0.958333
5 2TP 0.725 0.932432
6 VNP 0.721519 0.958904
7 VIB 0.621622 0.75
8 PYI 0.581395 0.887324
9 TDW 0.566667 0.972222
10 HTL 0.566667 0.958904
11 N1T 0.556818 0.985714
12 FTP 0.551724 0.835616
13 THV 0.548387 0.958904
14 TPW 0.546512 0.9
15 WWF 0.542553 0.933333
16 TD6 0.540816 0.921053
17 THY 0.536842 0.945946
18 TDL 0.53125 0.897436
19 THW 0.530612 0.958904
20 TD8 0.53 0.921053
21 TD9 0.53 0.921053
22 TDK 0.525773 0.921053
23 D7K 0.490566 0.909091
24 S1T 0.489362 0.887324
25 R1T 0.489362 0.887324
26 TPU 0.483146 0.842105
27 T5X 0.476636 0.897436
28 T6F 0.476636 0.897436
29 1U0 0.474227 0.84
30 8PA 0.459459 0.945946
31 TZD 0.451613 0.883117
32 TDM 0.443299 0.894737
33 THD 0.411765 0.839506
34 MP5 0.407895 0.676056
35 TD7 0.40566 0.85
36 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: 146
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)
1 1T9D P22 3.948e-06 0.61667
2 1YBH P22 2.199e-06 0.61166
3 1YBH P22 2.199e-06 0.61166
4 2VK4 TPP 4.266e-08 0.60822
5 2VK4 TPP 6.984e-08 0.59959
6 1QPB PYM 1.076e-07 0.57477
7 1QPB PYM 1.076e-07 0.57477
8 2UZ1 TPP 4.467e-07 0.56711
9 4RJK TPP 2.73e-07 0.56459
10 1QPB TPP 1.445e-07 0.56458
11 1QPB TPP 1.445e-07 0.56458
12 4RJK TPP 2.839e-07 0.56393
13 1ZPD DPX 2.386e-07 0.56154
14 4RJK TPP 3.616e-07 0.55984
15 2VBF TPP 3.478e-07 0.55528
16 1UPA TPP 9.623e-07 0.55368
17 3EYA TDP 1.011e-06 0.55283
18 4RJK TDL 3.246e-07 0.55136
19 3EYA TDP 1.662e-06 0.54412
20 2IHT TPP 1.734e-06 0.54338
21 2NXW TPP 2.724e-07 0.53531
22 2NXW TPP 2.724e-07 0.53531
23 3EYA TDP 4.144e-06 0.53316
24 3IAE D7K 7.055e-07 0.53165
25 1T9D PYD 6.71e-05 0.53016
26 2X7J TPP 1.641e-05 0.50405
27 2IHU TP9 1.664e-06 0.49491
28 3HWW AKG 0.00119 0.47385
29 1W55 GPP 0.02646 0.44833
30 3EXH TPP 0.001048 0.44519
31 3EXH TPP 0.001144 0.44354
32 2OZL TPP 0.001423 0.43942
33 1V5F FAD 0.002125 0.43763
34 1V5F TPP 0.002125 0.43763
35 1UMD TDP COI 0.0007445 0.43729
36 3CL5 SIO 0.01213 0.43392
37 3LE7 ADE 0.01117 0.43338
38 1KSK URA 0.01649 0.43296
39 2J9D ADP 0.001822 0.43126
40 3LE7 ADE 0.01346 0.43055
41 1W85 TDP 0.002303 0.43034
42 1M7G AV2 0.01134 0.42867
43 1W85 TDP 0.00255 0.42841
44 1YQT ADP 0.01408 0.42827
45 2X7I CIT 0.009544 0.42816
46 4RDN 6MD 0.01593 0.42679
47 2XDQ MGX 0.009206 0.42654
48 2OH5 CTP 0.01414 0.42632
49 2OH5 CTP 0.01414 0.42632
50 2OH5 CTP 0.01414 0.42632
51 3DVA TPW 0.001771 0.42521
52 4G28 0W8 0.01388 0.42411
53 1UMD TDP COI 0.001114 0.42408
54 3NCQ ATP 0.003231 0.42395
55 3NCQ ATP 0.003231 0.42395
56 1KC7 PPR 0.0217 0.42323
57 1KC7 PPR 0.0217 0.42323
58 2CYB TYR 0.01832 0.42271
59 3AI7 TPP 0.00175 0.42232
60 3AI7 TPP 0.001755 0.42227
61 2IYF UDP 0.0151 0.4222
62 2QZ3 XYP XYP XYP 0.01279 0.42173
63 3FSJ D7K 0.0005042 0.4217
64 2VF7 ADP 0.0108 0.42139
65 2VF7 ADP 0.0108 0.42139
66 4R8L ASP 0.01575 0.42124
67 1FNZ A2G 0.0217 0.42108
68 2O1S TDP 0.0077 0.42088
69 3AI7 TPP 0.001902 0.42086
70 3Q3H UDP 0.01974 0.42041
71 2AJ4 GLA 0.02045 0.41958
72 2QQC AG2 0.02059 0.41943
73 3AI7 TPP 0.002119 0.41897
74 1V3S ATP 0.005014 0.41891
75 1P4V GLY 0.02309 0.41887
76 2O1S TDP 0.008527 0.41879
77 1IZC PYR 0.01249 0.41845
78 2J9D AMP 0.007857 0.41689
79 3HQP OXL 0.02735 0.41674
80 2GPT TLA 0.02434 0.41654
81 3DVA TPW 0.002438 0.41651
82 2IYA UDP 0.01213 0.41511
83 2UZH IPE 0.02916 0.41365
84 2Z49 AMG 0.01522 0.41313
85 4WBD CIT 0.04041 0.41237
86 3HQP OXL 0.03171 0.41233
87 3WCS MAN NAG GAL 0.01975 0.41213
88 2VF7 ADP 0.01705 0.41156
89 1OJJ GLC GAL 0.0252 0.41059
90 1LYX PGA 0.01549 0.40996
91 1LYX PGA 0.01549 0.40996
92 4BQS K2Q 0.02716 0.40889
93 3OTH TYD 0.01389 0.40876
94 1HQL GLA MBG 0.0439 0.40862
95 1OJK GLC BGC 0.02781 0.40835
96 3U6K GDP 0.02393 0.40788
97 2Z9I GLY ALA THR VAL 0.03777 0.40765
98 3CQL NDG 0.03582 0.40743
99 2R68 SUP 0.03451 0.40737
100 2VF7 ADP 0.02071 0.40735
101 2VF7 ADP 0.02071 0.40735
102 1QS0 TDP 0.009204 0.4072
103 3FAS GLU 0.03552 0.40676
104 4HE2 AMP 0.02994 0.40667
105 1FHW I5P 0.0376 0.40642
106 1KJ1 MAN 0.02814 0.40633
107 1RP7 TZD 0.003764 0.40614
108 4E28 9MZ 0.03145 0.40563
109 1HQL GLA MBG 0.04958 0.40543
110 2O7B HC4 0.01945 0.40516
111 4E03 ADP 0.03226 0.40497
112 1PIE GLA 0.03899 0.40488
113 4I3G BGC 0.03259 0.40474
114 4RDN 6MD 0.03893 0.40454
115 1FWV SGA MAG FUC 0.0409 0.40451
116 4O48 ASP 0.04199 0.40434
117 1DAR GDP 0.02831 0.40415
118 2AWN ADP 0.03234 0.4038
119 2IYF UDP 0.01772 0.40373
120 2ACV UDP 0.02083 0.40372
121 1PBK RAP 0.04037 0.40369
122 1ZUW DGL 0.03448 0.40345
123 2JFN GLU 0.02974 0.40305
124 2OVW CBI 0.03519 0.40299
125 1VKF CIT 0.03697 0.40285
126 3WCS MAN NAG 0.04203 0.40274
127 2CHT TSA 0.04256 0.40245
128 2OVW CBI 0.03643 0.4022
129 1K6M AGS 0.01028 0.40206
130 3AI8 HNQ 0.04329 0.40205
131 1OF0 EBS 0.03761 0.40146
132 2OVW CBI 0.03768 0.40142
133 2AK3 AMP 0.04316 0.40142
134 1YRB GDP 0.01999 0.40124
135 3Q3H UDP 0.03235 0.40118
136 1FWY UD1 0.01258 0.40115
137 4KSY 1SY 0.04518 0.40105
138 1FWY UD1 0.01272 0.40095
139 4JBL MET 0.04538 0.40094
140 2IYA UDP 0.01737 0.40091
141 3S2U UD1 0.01096 0.40085
142 4USI ATP 0.01104 0.40071
143 1XKV ATP 0.02416 0.40058
144 2PUZ NIG 0.04658 0.40032
145 4NZ6 DLY 0.04457 0.40022
146 4U36 TNR 0.04955 0.40018
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)
Pocket No.: 3; Query (leader) PDB : 2C42; Ligand: TPP; Similar sites found: 146
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)
1 1T9D P22 3.948e-06 0.61667
2 1YBH P22 2.199e-06 0.61166
3 1YBH P22 2.199e-06 0.61166
4 2VK4 TPP 4.266e-08 0.60822
5 2VK4 TPP 6.984e-08 0.59959
6 1QPB PYM 1.076e-07 0.57477
7 1QPB PYM 1.076e-07 0.57477
8 2UZ1 TPP 4.467e-07 0.56711
9 4RJK TPP 2.73e-07 0.56459
10 1QPB TPP 1.445e-07 0.56458
11 1QPB TPP 1.445e-07 0.56458
12 4RJK TPP 2.839e-07 0.56393
13 1ZPD DPX 2.386e-07 0.56154
14 4RJK TPP 3.616e-07 0.55984
15 2VBF TPP 3.478e-07 0.55528
16 1UPA TPP 9.623e-07 0.55368
17 3EYA TDP 1.011e-06 0.55283
18 4RJK TDL 3.246e-07 0.55136
19 3EYA TDP 1.662e-06 0.54412
20 2IHT TPP 1.734e-06 0.54338
21 2NXW TPP 2.724e-07 0.53531
22 2NXW TPP 2.724e-07 0.53531
23 3EYA TDP 4.144e-06 0.53316
24 3IAE D7K 7.055e-07 0.53165
25 1T9D PYD 6.71e-05 0.53016
26 2X7J TPP 1.641e-05 0.50405
27 2IHU TP9 1.664e-06 0.49491
28 3HWW AKG 0.00119 0.47385
29 1W55 GPP 0.02646 0.44833
30 3EXH TPP 0.001048 0.44519
31 3EXH TPP 0.001144 0.44354
32 2OZL TPP 0.001423 0.43942
33 1V5F FAD 0.002125 0.43763
34 1V5F TPP 0.002125 0.43763
35 1UMD TDP COI 0.0007445 0.43729
36 3CL5 SIO 0.01213 0.43392
37 3LE7 ADE 0.01117 0.43338
38 1KSK URA 0.01649 0.43296
39 2J9D ADP 0.001822 0.43126
40 3LE7 ADE 0.01346 0.43055
41 1W85 TDP 0.002303 0.43034
42 1M7G AV2 0.01134 0.42867
43 1W85 TDP 0.00255 0.42841
44 1YQT ADP 0.01408 0.42827
45 2X7I CIT 0.009544 0.42816
46 4RDN 6MD 0.01593 0.42679
47 2XDQ MGX 0.009206 0.42654
48 2OH5 CTP 0.01414 0.42632
49 2OH5 CTP 0.01414 0.42632
50 2OH5 CTP 0.01414 0.42632
51 3DVA TPW 0.001771 0.42521
52 4G28 0W8 0.01388 0.42411
53 1UMD TDP COI 0.001114 0.42408
54 3NCQ ATP 0.003231 0.42395
55 3NCQ ATP 0.003231 0.42395
56 1KC7 PPR 0.0217 0.42323
57 1KC7 PPR 0.0217 0.42323
58 2CYB TYR 0.01832 0.42271
59 3AI7 TPP 0.00175 0.42232
60 3AI7 TPP 0.001755 0.42227
61 2IYF UDP 0.0151 0.4222
62 2QZ3 XYP XYP XYP 0.01279 0.42173
63 3FSJ D7K 0.0005042 0.4217
64 2VF7 ADP 0.0108 0.42139
65 2VF7 ADP 0.0108 0.42139
66 4R8L ASP 0.01575 0.42124
67 1FNZ A2G 0.0217 0.42108
68 2O1S TDP 0.0077 0.42088
69 3AI7 TPP 0.001902 0.42086
70 3Q3H UDP 0.01974 0.42041
71 2AJ4 GLA 0.02045 0.41958
72 2QQC AG2 0.02059 0.41943
73 3AI7 TPP 0.002119 0.41897
74 1V3S ATP 0.005014 0.41891
75 1P4V GLY 0.02309 0.41887
76 2O1S TDP 0.008527 0.41879
77 1IZC PYR 0.01249 0.41845
78 2J9D AMP 0.007857 0.41689
79 3HQP OXL 0.02735 0.41674
80 2GPT TLA 0.02434 0.41654
81 3DVA TPW 0.002438 0.41651
82 2IYA UDP 0.01213 0.41511
83 2UZH IPE 0.02916 0.41365
84 2Z49 AMG 0.01522 0.41313
85 4WBD CIT 0.04041 0.41237
86 3HQP OXL 0.03171 0.41233
87 3WCS MAN NAG GAL 0.01975 0.41213
88 2VF7 ADP 0.01705 0.41156
89 1OJJ GLC GAL 0.0252 0.41059
90 1LYX PGA 0.01549 0.40996
91 1LYX PGA 0.01549 0.40996
92 4BQS K2Q 0.02716 0.40889
93 3OTH TYD 0.01389 0.40876
94 1HQL GLA MBG 0.0439 0.40862
95 1OJK GLC BGC 0.02781 0.40835
96 3U6K GDP 0.02393 0.40788
97 2Z9I GLY ALA THR VAL 0.03777 0.40765
98 3CQL NDG 0.03582 0.40743
99 2R68 SUP 0.03451 0.40737
100 2VF7 ADP 0.02071 0.40735
101 2VF7 ADP 0.02071 0.40735
102 1QS0 TDP 0.009204 0.4072
103 3FAS GLU 0.03552 0.40676
104 4HE2 AMP 0.02994 0.40667
105 1FHW I5P 0.0376 0.40642
106 1KJ1 MAN 0.02814 0.40633
107 1RP7 TZD 0.003764 0.40614
108 4E28 9MZ 0.03145 0.40563
109 1HQL GLA MBG 0.04958 0.40543
110 2O7B HC4 0.01945 0.40516
111 4E03 ADP 0.03226 0.40497
112 1PIE GLA 0.03899 0.40488
113 4I3G BGC 0.03259 0.40474
114 4RDN 6MD 0.03893 0.40454
115 1FWV SGA MAG FUC 0.0409 0.40451
116 4O48 ASP 0.04199 0.40434
117 1DAR GDP 0.02831 0.40415
118 2AWN ADP 0.03234 0.4038
119 2IYF UDP 0.01772 0.40373
120 2ACV UDP 0.02083 0.40372
121 1PBK RAP 0.04037 0.40369
122 1ZUW DGL 0.03448 0.40345
123 2JFN GLU 0.02974 0.40305
124 2OVW CBI 0.03519 0.40299
125 1VKF CIT 0.03697 0.40285
126 3WCS MAN NAG 0.04203 0.40274
127 2CHT TSA 0.04256 0.40245
128 2OVW CBI 0.03643 0.4022
129 1K6M AGS 0.01028 0.40206
130 3AI8 HNQ 0.04329 0.40205
131 1OF0 EBS 0.03761 0.40146
132 2OVW CBI 0.03768 0.40142
133 2AK3 AMP 0.04316 0.40142
134 1YRB GDP 0.01999 0.40124
135 3Q3H UDP 0.03235 0.40118
136 1FWY UD1 0.01258 0.40115
137 4KSY 1SY 0.04518 0.40105
138 1FWY UD1 0.01272 0.40095
139 4JBL MET 0.04538 0.40094
140 2IYA UDP 0.01737 0.40091
141 3S2U UD1 0.01096 0.40085
142 4USI ATP 0.01104 0.40071
143 1XKV ATP 0.02416 0.40058
144 2PUZ NIG 0.04658 0.40032
145 4NZ6 DLY 0.04457 0.40022
146 4U36 TNR 0.04955 0.40018
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)
Feedback