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Receptor
PDB id Resolution Class Description Source Keywords
3DDN 2.4 Å EC: 1.1.1.95 CRYSTAL STRUCTURE OF HYDROXYPYRUVIC ACID PHOSPHATE BOUND D-3 PHOSPHOGLYCERATE DEHYDROGENASE IN MYCOBACTERIUM TUBERCULOSI MYCOBACTERIUM TUBERCULOSIS OXIDOREDUCTASE PHOSPHOGLYCERATE DEHYDROGENASE SERINE BIOSYAMINO-ACID BIOSYNTHESIS NAD
Ref.: STRUCTURAL ANALYSIS OF SUBSTRATE AND EFFECTOR BINDI MYCOBACTERIUM TUBERCULOSIS D-3-PHOSPHOGLYCERATE DEHYDROGENASE BIOCHEMISTRY V. 47 8271 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
HPV B:600;
Valid;
none;
submit data
184.041 C3 H5 O7 P C(C(=...
TLA A:530;
B:530;
B:531;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
150.087 C4 H6 O6 [C@@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3DDN 2.4 Å EC: 1.1.1.95 CRYSTAL STRUCTURE OF HYDROXYPYRUVIC ACID PHOSPHATE BOUND D-3 PHOSPHOGLYCERATE DEHYDROGENASE IN MYCOBACTERIUM TUBERCULOSI MYCOBACTERIUM TUBERCULOSIS OXIDOREDUCTASE PHOSPHOGLYCERATE DEHYDROGENASE SERINE BIOSYAMINO-ACID BIOSYNTHESIS NAD
Ref.: STRUCTURAL ANALYSIS OF SUBSTRATE AND EFFECTOR BINDI MYCOBACTERIUM TUBERCULOSIS D-3-PHOSPHOGLYCERATE DEHYDROGENASE BIOCHEMISTRY V. 47 8271 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3DDN - HPV C3 H5 O7 P C(C(=O)C(=....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3DDN - HPV C3 H5 O7 P C(C(=O)C(=....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3DDN - HPV C3 H5 O7 P C(C(=O)C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: HPV; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 HPV 1 1
2 PGA 0.555556 0.903226
3 13P 0.4375 0.90625
4 PGH 0.424242 0.636364
5 PPR 0.413793 0.903226
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3DDN; Ligand: HPV; Similar sites found with APoc: 152
This union binding pocket(no: 1) in the query (biounit: 3ddn.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 6FDF SAH 0.898204
2 3EYA FAD 1.32576
3 2WOJ ADP ALF 1.41243
4 3ZS9 ADP ALF 1.41243
5 1CDO NAD 1.60428
6 1FEC FAD 1.63265
7 1GR0 NAD 1.63488
8 1V6A TRE 1.80723
9 1V59 NAD 1.88285
10 1QO8 FAD 1.89394
11 5VN0 FAD 1.9305
12 1BZL FAD 2.05761
13 1H6C NDP 2.07852
14 1H6C SIN 2.07852
15 1Q9I TEO 2.08333
16 1Q9I FAD 2.08333
17 1F0X FAD 2.08333
18 1F8G NAD 2.08333
19 1GTE FAD 2.27273
20 5L9G MO0 2.2792
21 1RYD NDP 2.32558
22 1ZH8 NAP 2.35294
23 1QMG APX 2.48092
24 5FBN 5WF 2.58303
25 3IO3 ADP 2.58621
26 3FXU TSU 2.62295
27 5JE8 NAD 2.64901
28 3IHG FAD 2.65152
29 1D7O NAD 2.6936
30 1D7O TCL 2.6936
31 4JBI NDP 2.7027
32 4MP8 MLI 2.94985
33 4MP8 NAD 2.94985
34 1M2W NAD 3.0426
35 5D85 P1T 3.06748
36 1X87 NAD 3.0853
37 4EU7 CIT 3.11284
38 4EU7 COA 3.11284
39 6GNA FAD 3.125
40 2JFN GLU 3.15789
41 5TUF FAD 3.17848
42 3LZW NAP 3.31325
43 5A1S FLC 3.34821
44 2GZM DGL 3.37079
45 1WP4 NDP 3.46021
46 5DX9 T6P 3.48101
47 3B9Z CO2 3.60825
48 2IID PHE 3.61446
49 2IID FAD 3.61446
50 5NUE NAD 3.61446
51 5NUF NAD 3.61446
52 2VT3 ATP 3.72093
53 5OCM NAP 3.78007
54 5A04 BGC 3.83481
55 5A04 NDP 3.83481
56 6CEP NAD 3.89222
57 6CEP OXM 3.89222
58 4D5G FAD 3.97727
59 4D5G TPP 3.97727
60 1IWE IMP 4.15755
61 1W8S FBP 4.18251
62 2R4J FAD 4.19162
63 2R4J 13P 4.19162
64 2GLX NDP 4.21687
65 4YT4 FE9 4.26667
66 3HDY FDA 4.28212
67 3HDY FAD 4.28212
68 3HDY GDU 4.28212
69 4UTG ANP 4.33526
70 1MUU NAD 4.3578
71 3OJO NAD 4.40835
72 1MV8 NAD 4.58716
73 2IV3 UDP 4.67836
74 5VKT NAP 4.69613
75 2DT5 NAD 4.73934
76 4EN4 ATP 4.80769
77 4EN4 GT0 4.80769
78 4EN4 GT1 4.80769
79 1H82 FAD 4.87288
80 1H82 GZZ 4.87288
81 2RGJ FAD 4.97512
82 1P31 EPU 5.05263
83 1P3D UMA 5.05263
84 1P4A PCP 5.26316
85 5U5G NAP 5.42373
86 3WV8 ATP 5.50459
87 4E13 NAD 5.65371
88 1Y8Q ATP 5.68182
89 2DKH FAD 5.68182
90 9LDB NAD 5.72289
91 9LDT NAD 5.72289
92 2F1K NAP 5.73477
93 3H8V ATP 5.82192
94 3S5W FAD 5.83153
95 3T31 DCQ 6.06061
96 3T31 FAD 6.06061
97 1GQ2 NAP 6.06061
98 3DAG FEG 6.14525
99 3VYW SAM 6.16883
100 4AUT FAD 6.19658
101 2BEK ATP 6.22568
102 2VVT I24 6.43939
103 1V8B NAD 6.88935
104 4RDH AMP 6.94444
105 4RDI ATP 6.94444
106 1OMO NAD 7.14286
107 2PT9 2MH 7.16511
108 2PT9 S4M 7.16511
109 4II2 ATP 7.22892
110 1UWK NAD 7.38636
111 1UWK URO 7.38636
112 4UP4 NDG 7.4813
113 1WOQ BGC 7.49064
114 5XKT GNP 7.5
115 1YQD NAP 7.65027
116 5GUF CTP 7.69231
117 4D3F NAP 7.74194
118 4OM8 NAD 7.76699
119 4XVU ATP 7.82609
120 4XTR ATP 7.82609
121 4XTR ADP 7.82609
122 4JJF N2I 7.84884
123 4JJF FE9 7.84884
124 1M5W DXP 8.23045
125 3QJ4 FAD 8.47953
126 1HYH NAD 8.73786
127 5YU3 PRO 9.01163
128 5YU3 NAD 9.01163
129 1NM5 NAD 9.35961
130 5YEC ATP 9.41177
131 4ZOH MCN 10.119
132 1E6E FAD 10.1562
133 2OOR NAD 10.9195
134 5OJL TXP 11.0738
135 1I36 NAP 11.7424
136 2HMT NAI 11.8056
137 1CF2 NAP 11.8694
138 4C0X FMN 13.7931
139 4C0X AQN 13.7931
140 5XVH NAP 14.0523
141 4D79 ATP 14.1304
142 4RFM 3P6 16.9173
143 1T3Q MCN 17.2619
144 4HSU FAD 20
145 1LSS NAD 24.2857
146 5X9D 80F 25.9868
147 4ZGS NAD 36.2694
148 5Z21 OXM 36.8715
149 5Z20 OXM 39.1304
150 3KB6 LAC 41.018
151 2GCG NDP 43.9394
152 4E5N NAD 45.4545
Pocket No.: 2; Query (leader) PDB : 3DDN; Ligand: HPV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3ddn.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
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