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 4 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: 210
This union binding pocket(no: 1) in the query (biounit: 3ddn.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1PTR PRB 0.008581 0.40159 None
2 1H16 PYR 0.0021 0.43578 0.94697
3 4WBD ADP 0.0007359 0.44779 1.32576
4 2NCD ADP 0.0001003 0.46746 1.42857
5 2ZWS PLM 0.004201 0.44892 1.51515
6 1T10 F6P 0.004002 0.40337 1.51515
7 3A8U PLP 0.009891 0.41478 1.55902
8 2J0W ASP 0.005579 0.4097 1.55902
9 3ZGE ASP 0.01156 0.4023 1.61616
10 2DWU DGL 0.0009487 0.40698 1.81159
11 1PEA ACM 0.008515 0.40831 1.81818
12 2YIV YIV 0.002579 0.43176 1.89394
13 2YIV NBN 0.005105 0.41138 1.89394
14 4R33 TRP 0.004119 0.44269 1.90476
15 4R33 SAH 0.004119 0.44269 1.90476
16 1FDJ 2FP 0.002364 0.42402 1.92837
17 3L24 GOA 0.005275 0.42541 1.93424
18 2RCN GDP 0.0001033 0.43521 1.95531
19 3UN3 G16 0.005819 0.45819 2.00501
20 1M1B SPV 0.001397 0.42168 2.0339
21 2NVK NAP 0.0008294 0.41918 2.04918
22 2W8Q SIN 0.001593 0.43327 2.05339
23 3UEC ALA ARG TPO LYS 0.009312 0.40005 2.05479
24 1A59 CIT 0.008669 0.4014 2.1164
25 1NX4 AKG 0.0008977 0.42937 2.1978
26 3QV9 QV7 0.000262 0.45078 2.20441
27 4KCT PYR 0.0008822 0.41014 2.20441
28 2YVF FAD 0.002197 0.47884 2.20588
29 2YVF NAD 0.002274 0.47884 2.20588
30 4M5P MLA 0.0004775 0.48561 2.2113
31 4M5P 23W 0.008886 0.40747 2.2113
32 4GYW UDP 0.011 0.42204 2.27273
33 2WQP WQP 0.0004878 0.47585 2.29226
34 1RYD GLC 0.0004216 0.45006 2.32558
35 1RRC ADP 0.001469 0.44778 2.32558
36 1ZH8 NAP 0.04002 0.40331 2.35294
37 3SBZ MLI 0.0003359 0.48183 2.38095
38 4JCA CIT 0.001206 0.46573 2.39521
39 3O03 GCO 0.0008927 0.46182 2.4055
40 1KTC NGA 0.001926 0.40665 2.46914
41 3HZL 6PC 0.003114 0.43623 2.51889
42 2Y0I AKG 0.001682 0.41845 2.55682
43 2F7C CCU 0.001469 0.42081 2.57511
44 3P3N AKG 0.001259 0.43029 2.5788
45 2XUM OGA 0.001276 0.43006 2.5788
46 4B7E OGA 0.001575 0.4196 2.5788
47 1QH9 LAC 0.001299 0.42973 2.58621
48 4W6Z ETF 0.006059 0.42257 2.59366
49 3FW3 GLC 0.04433 0.41642 2.63158
50 1KC7 PPR 0.00431 0.41456 2.84091
51 1R37 ETX 0.00279 0.41592 2.88184
52 4LIT AKG 0.002825 0.40943 2.9484
53 2V5E SCR 0.007585 0.4262 2.9703
54 4JLV ADP 0.0199 0.40936 2.97398
55 2EB5 OXL 0.00116 0.43178 2.99625
56 2BLE 5GP 0.008156 0.45035 2.99728
57 1XHL NDP 0.007033 0.43088 3.0303
58 1G0V NAG 0.002011 0.45618 3.03951
59 1SOW OXL 0.006722 0.42044 3.04878
60 1QO0 BMD 0.00298 0.41473 3.06122
61 4N02 FNR 0.006798 0.44982 3.08123
62 3UCJ AZM 0.0007291 0.41201 3.0837
63 3P7I P7I 0.001523 0.41109 3.11526
64 3TXO 07U 0.00007043 0.41866 3.11615
65 4N7U 2JA 0.0008098 0.46381 3.15789
66 2Q8H TF4 0.009163 0.41407 3.1941
67 1SS4 GSH 0.01307 0.42007 3.26797
68 1SS4 CIT 0.04144 0.40092 3.26797
69 1U5V ATP 0.0006654 0.49105 3.2967
70 2YD6 FLC 0.002834 0.48255 3.30189
71 2CW6 3HG 0.008522 0.41556 3.3557
72 1RYI GOA 0.01048 0.43468 3.40314
73 2Y6P CTP 0.0005607 0.40951 3.4188
74 1G8S MET 0.005499 0.40365 3.47826
75 2BOI MFU 0.001999 0.40657 3.53982
76 4K7O EKZ 0.003721 0.41733 3.57143
77 3B9Z CO2 0.004157 0.41386 3.60825
78 4FGC PQ0 0.002926 0.40882 3.63636
79 4AF5 CIT 0.0003722 0.4523 3.68421
80 1Q6O LG6 0.0001653 0.4083 3.7037
81 3C1O NAP 0.007764 0.41943 3.73832
82 2DUA OXL 0.01246 0.40389 3.7931
83 1P9B HDA 0.0004408 0.44173 3.84615
84 5YAS FAC 0.002155 0.42308 3.89105
85 2P69 PLP 0.0009286 0.42878 3.92157
86 3WCS MAN NAG 0.001167 0.41478 3.93701
87 3MD0 GDP 0.0004282 0.4234 3.94366
88 1OIK AKG 0.00043 0.4497 3.98671
89 1E4E PHY 0.0001649 0.40072 4.08163
90 1T3D CYS 0.002488 0.4249 4.15225
91 3BLI PYR 0.0009578 0.44284 4.1543
92 5EQU AKG 0.01032 0.40453 4.2623
93 3U7Y FLC 0.03873 0.40344 4.28571
94 3UDG TMP 0.0004751 0.47473 4.31894
95 1JGS SAL 0.007125 0.43696 4.34783
96 1GJW GLC 0.004499 0.41375 4.35606
97 1O68 KIV 0.002178 0.40336 4.36364
98 1RTF BEN 0.02486 0.41105 4.36508
99 2FWP CIT 0.005108 0.43595 4.37158
100 2FWP ICR 0.01488 0.41936 4.37158
101 1LYX PGA 0.0001607 0.40672 4.43548
102 2F2U M77 0.0001719 0.42611 4.47761
103 3B8I OXL 0.002314 0.45173 4.52962
104 3OAI MAL 0.007375 0.40771 4.53649
105 1Y9Q MED 0.004582 0.40695 4.54545
106 3SCH TB6 0.005009 0.40534 4.54545
107 1ZZ7 S0H 0.002508 0.40082 4.54545
108 2C31 ADP 0.007147 0.45952 4.57746
109 2C31 TZD 0.007342 0.45952 4.57746
110 1GVF PGH 0.002287 0.40391 4.8951
111 1Y1A GSH 0.01269 0.42813 4.91803
112 3TFC PEP 0.001634 0.40973 4.93506
113 1YHM AHD 0.004181 0.40261 4.97238
114 1UW1 ADP 0.003414 0.40613 5
115 1YOA FMN 0.002121 0.46437 5.03145
116 3ICV NAG 0.007164 0.44246 5.06329
117 1X54 4AD 0.001256 0.4543 5.06912
118 2C5S AMP 0.001396 0.40509 5.08475
119 4N7C AEF 0.002039 0.42864 5.11364
120 3CBG FER 0.0005618 0.4713 5.17241
121 1IYE PGU 0.005485 0.43455 5.17799
122 2X2T GAL NGA 0.002747 0.43879 5.22876
123 3I0O ADP 0.0007186 0.40513 5.30973
124 2R00 OEG 0.002841 0.4224 5.35714
125 1XX4 BAM 0.005537 0.42442 5.36398
126 1Y7P RIP 0.009918 0.40531 5.38117
127 2PYU IMP 0.0002913 0.44893 5.47945
128 1NML CIT 0.002146 0.40437 5.52147
129 2VWT PYR 0.001932 0.42965 5.61798
130 3R51 MMA 0.00124 0.45509 5.625
131 1BTN I3P 0.002675 0.46604 5.66038
132 3VPD BUA 0.006085 0.44894 5.69395
133 3VPD CIT 0.005193 0.43435 5.69395
134 1C3V PDC 0.0005059 0.43934 5.71429
135 2PTZ PAH 0.0002596 0.46928 5.78704
136 3E4O SIN 0.001644 0.41885 5.90164
137 3IHB TRS 0.001435 0.47891 5.92105
138 2VQ5 HBA 0.002112 0.42798 5.97015
139 3ZPG 5GP 0.002249 0.44289 6.02094
140 2XDQ MGX 0.003896 0.43163 6.06654
141 3DAG FEG 0.0186 0.41801 6.14525
142 2DTJ THR 0.000877 0.40155 6.17978
143 2JFV FLC 0.003663 0.411 6.18557
144 4BI7 PGA 0.0007296 0.41099 6.22568
145 1RQH PYR 0.0006805 0.44926 6.25
146 1O9U ADZ 0.01613 0.40243 6.28571
147 2DVZ GLU 0.0003301 0.4175 6.36943
148 1WTC ACP 0.006003 0.40832 6.50155
149 1RZM E4P 0.003475 0.41861 6.50888
150 1HQL GLA MBG 0.00331 0.41953 6.61479
151 2JBH 5GP 0.000647 0.41316 6.66667
152 4B16 NAG 0.003392 0.44351 6.76692
153 3MAG 3MA 0.01827 0.40722 6.84039
154 3ZLM ANP 0.0135 0.4006 6.91489
155 3SQG COM 0.0189 0.40649 6.92841
156 2XI7 XI7 0.000703 0.48932 7.06522
157 1WHT BZS 0.004473 0.40739 7.42188
158 2BO4 FLC 0.002662 0.42363 7.55667
159 2ZYF AKG 0.001554 0.40119 7.59162
160 3UBW 6SP 0.005956 0.44626 7.66284
161 3PNA CMP 0.000502 0.41683 7.79221
162 1HFA PIO 0.002691 0.49482 7.95848
163 2XBP ATP 0.001771 0.47304 7.9646
164 1ULE GLA GAL NAG 0.01182 0.40186 8
165 2BZ1 TAU 0.006159 0.44026 8.16327
166 3F81 STT 0.007953 0.41698 8.19672
167 1NU4 MLA 0.004274 0.44853 8.24742
168 4G1V FAD 0.004831 0.43301 8.27068
169 4A3X LAT 0.0005795 0.47066 8.37004
170 4RJK PYR 0.01636 0.41809 8.52273
171 4JEJ 1GP 0.0002548 0.4109 8.60656
172 3RF4 FUN 0.002526 0.40445 8.62069
173 4B9E FAH 0.003811 0.41688 8.63787
174 1NXJ GLV 0.001158 0.40418 8.74317
175 1TDF FAD 0.001139 0.48261 8.86076
176 1TDF NAP 0.002449 0.48261 8.86076
177 1H9G COA MYR 0.001465 0.45462 9.0535
178 4IXW IXW 0.00008342 0.44551 9.05512
179 1SC3 MLI 0.0002063 0.48124 9.09091
180 3S9K CIT 0.0009346 0.50083 9.32203
181 1Y2W NAG 0.003222 0.41332 9.85915
182 2XRH NIO 0.002674 0.42354 10
183 3UIE ANP 0.0006686 0.40288 10
184 2Q1A 2KT 0.002306 0.41937 10.2389
185 1XE7 GUN 0.002177 0.44356 10.3448
186 3I7S PYR 0.002133 0.43548 10.9589
187 1JN2 SFP 0.002466 0.48539 10.9705
188 4JWX 1N4 0.002665 0.4009 11.4286
189 1UWZ THU 0.003305 0.42263 11.7647
190 3L6R MLI 0.001653 0.43259 12.7168
191 4G28 0W8 0.0006338 0.41525 12.7517
192 3QDX A2G GAL 0.006925 0.41237 13.2867
193 3QDT A2G GAL 0.01061 0.40398 13.2867
194 3I6B KDO 0.001127 0.41452 13.3333
195 1H2M OGA 0.001113 0.43252 13.4615
196 1Z42 HBA 0.0005656 0.50247 14.2012
197 1Z44 NPO 0.001762 0.46857 14.2012
198 1NME 159 0.0006564 0.46811 14.3836
199 1B74 DGN 0.001642 0.44061 14.5669
200 2O66 FLC 0.003136 0.40762 15.5556
201 2QLX RM4 0.004492 0.41379 15.7407
202 2H6B 3C4 0.0187 0.43002 16.8
203 1H2K OGA 0.001105 0.43266 17.0732
204 2VKL MLT 0.01872 0.40669 18.8889
205 2W1A TSA 0.005647 0.40581 18.8889
206 1ECM TSA 0.001666 0.40082 22.0183
207 1JAC AMG 0.006717 0.42882 24.0602
208 1DL7 NCH 0.01799 0.41592 25
209 1DXY COI 0.006119 0.42237 39.3393
210 3KB6 LAC 0.001918 0.44343 41.018
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