NPASS Natural Product

Natural Product: NPC38891

Natural Product ID:	NPC38891
Common Name:	D-Hydroxyglutarate
IUPAC Name:	(2R)-2-hydroxypentanedioic acid
Synonyms:	(R)-2-Hydroxypentanedioic Acid; D-Hydroxyglutarate
Molecular Formula:	C5H8O5
Standard InCHIKey:	HWXBTNAVRSUOJR-GSVOUGTGSA-N
Standard InCHI:	InChI=1S/C5H8O5/c6-3(5(9)10)1-2-4(7)8/h3,6H,1-2H2,(H,7,8)(H,9,10)/t3-/m1/s1
Canonical SMILES:	OC(=O)CC[C@H](C(=O)O)O
First Find Year:
Max Developmental Stage:
Synthetic Gene Cluster:	;

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Reference
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	blood	PMID[8134166]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	saliva	PMID[22308371]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	urine	PMID[8087979]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	Faeces	PMID[20669995]
NPO4011	Chlamydomonas reinhardtii	Species	Chlamydomonadaceae	Eukaryota		PMID[25515814]

Biological Activity

Activity Type	# Activity
IC50	4

Activity Type	# Activity
Individual Protein	4

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT532	Individual Protein	Lysine-specific demethylase 4A	Homo sapiens	IC50	=	24000	nM	21955276
NPT2724	Individual Protein	Lysine-specific demethylase 2A	Homo sapiens	IC50	=	106000	nM	21955276
NPT2725	Individual Protein	Lysine-specific demethylase 4C	Homo sapiens	IC50	=	79000	nM	21955276
NPT1510	Individual Protein	Alpha-ketoglutarate-dependent dioxygenase FTO	Homo sapiens	IC50	>	1000000	nM	23547775

Similar Natural Products in NPASS

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC38891 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	971
0.1-0.2	8676
0.2-0.3	12236
0.3-0.4	7247
0.4-0.5	1447
0.5-0.6	227
0.6-0.7	45
0.7-0.8	34
0.8-0.85	5
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC242655
0.8367	Intermediate Similarity	NPC19676
0.8367	Intermediate Similarity	NPC323401
0.82	Intermediate Similarity	NPC6883
0.8163	Intermediate Similarity	NPC277878
0.8	Intermediate Similarity	NPC196612
0.7955	Intermediate Similarity	NPC35661
0.7826	Intermediate Similarity	NPC270088
0.7778	Intermediate Similarity	NPC259982
0.7778	Intermediate Similarity	NPC313565
0.7778	Intermediate Similarity	NPC228782
0.7708	Intermediate Similarity	NPC172086
0.7708	Intermediate Similarity	NPC247546
0.7674	Intermediate Similarity	NPC128713
0.7619	Intermediate Similarity	NPC5505
0.7609	Intermediate Similarity	NPC319680
0.7556	Intermediate Similarity	NPC97444
0.7556	Intermediate Similarity	NPC100742
0.7556	Intermediate Similarity	NPC192402
0.7556	Intermediate Similarity	NPC19044
0.7556	Intermediate Similarity	NPC24751
0.7556	Intermediate Similarity	NPC121018
0.7551	Intermediate Similarity	NPC293378
0.7551	Intermediate Similarity	NPC46254
0.7407	Intermediate Similarity	NPC220922
0.7407	Intermediate Similarity	NPC293692
0.7333	Intermediate Similarity	NPC320331
0.7317	Intermediate Similarity	NPC125575
0.7308	Intermediate Similarity	NPC65985
0.7222	Intermediate Similarity	NPC198377
0.7143	Intermediate Similarity	NPC323945
0.7111	Intermediate Similarity	NPC222792
0.7111	Intermediate Similarity	NPC316217
0.7091	Intermediate Similarity	NPC61567
0.7069	Intermediate Similarity	NPC88898
0.7069	Intermediate Similarity	NPC106216
0.7045	Intermediate Similarity	NPC206924
0.7037	Intermediate Similarity	NPC60830
0.7037	Intermediate Similarity	NPC68743
0.7018	Intermediate Similarity	NPC320296
0.6964	Remote Similarity	NPC179624
0.6957	Remote Similarity	NPC240109
0.6863	Remote Similarity	NPC328954
0.6829	Remote Similarity	NPC198126
0.678	Remote Similarity	NPC258690
0.678	Remote Similarity	NPC317651
0.6744	Remote Similarity	NPC127142
0.6667	Remote Similarity	NPC76217
0.6667	Remote Similarity	NPC317945
0.6667	Remote Similarity	NPC307739
0.6667	Remote Similarity	NPC149070
0.6667	Remote Similarity	NPC127074
0.6667	Remote Similarity	NPC187058
0.6667	Remote Similarity	NPC197207
0.6667	Remote Similarity	NPC182541
0.6607	Remote Similarity	NPC3547
0.6591	Remote Similarity	NPC317203
0.6591	Remote Similarity	NPC325165
0.6522	Remote Similarity	NPC325454
0.6444	Remote Similarity	NPC24967
0.6444	Remote Similarity	NPC159089
0.6444	Remote Similarity	NPC103612
0.6364	Remote Similarity	NPC7814
0.6349	Remote Similarity	NPC57788
0.6349	Remote Similarity	NPC32148
0.6349	Remote Similarity	NPC53879
0.6327	Remote Similarity	NPC310220
0.6304	Remote Similarity	NPC109026
0.6296	Remote Similarity	NPC100096
0.6222	Remote Similarity	NPC293908
0.6222	Remote Similarity	NPC250870
0.6222	Remote Similarity	NPC191084
0.6222	Remote Similarity	NPC66052
0.6222	Remote Similarity	NPC325034
0.6222	Remote Similarity	NPC86412
0.6222	Remote Similarity	NPC316685
0.6222	Remote Similarity	NPC192065
0.6222	Remote Similarity	NPC168052
0.619	Remote Similarity	NPC174368
0.617	Remote Similarity	NPC38930
0.6136	Remote Similarity	NPC328710
0.6136	Remote Similarity	NPC18224
0.6087	Remote Similarity	NPC321699
0.6087	Remote Similarity	NPC1037
0.6	Remote Similarity	NPC17935
0.5965	Remote Similarity	NPC23155
0.5965	Remote Similarity	NPC53463
0.5965	Remote Similarity	NPC469937
0.5965	Remote Similarity	NPC320588
0.5952	Remote Similarity	NPC33415
0.5952	Remote Similarity	NPC236709
0.5952	Remote Similarity	NPC301586
0.5909	Remote Similarity	NPC212144
0.5849	Remote Similarity	NPC324004
0.5849	Remote Similarity	NPC328497
0.5833	Remote Similarity	NPC322855
0.5814	Remote Similarity	NPC270334
0.5814	Remote Similarity	NPC292641
0.58	Remote Similarity	NPC325307
0.58	Remote Similarity	NPC322956
0.5778	Remote Similarity	NPC99700
0.5778	Remote Similarity	NPC175342
0.5745	Remote Similarity	NPC134782
0.5741	Remote Similarity	NPC200618
0.5741	Remote Similarity	NPC131770
0.5741	Remote Similarity	NPC106872
0.5714	Remote Similarity	NPC268243
0.5714	Remote Similarity	NPC325773
0.5714	Remote Similarity	NPC320326
0.5714	Remote Similarity	NPC94368
0.5692	Remote Similarity	NPC241949
0.5686	Remote Similarity	NPC213159
0.5686	Remote Similarity	NPC86191
0.5686	Remote Similarity	NPC317182
0.5686	Remote Similarity	NPC291502
0.5686	Remote Similarity	NPC298699
0.5686	Remote Similarity	NPC320189
0.5686	Remote Similarity	NPC134252
0.5686	Remote Similarity	NPC289686
0.5672	Remote Similarity	NPC28526
0.5667	Remote Similarity	NPC43169
0.5667	Remote Similarity	NPC93861
0.5667	Remote Similarity	NPC327895
0.5667	Remote Similarity	NPC112224
0.5667	Remote Similarity	NPC323436
0.566	Remote Similarity	NPC133771
0.5652	Remote Similarity	NPC227267
0.5652	Remote Similarity	NPC307027
0.5636	Remote Similarity	NPC304162
0.5614	Remote Similarity	NPC317680
0.561	Remote Similarity	NPC165122
0.56	Remote Similarity	NPC88278
0.56	Remote Similarity	NPC227707
0.56	Remote Similarity	NPC111882
0.56	Remote Similarity	NPC266553
0.56	Remote Similarity	NPC102981
0.56	Remote Similarity	NPC99573

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC38891 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	1893
0.1-0.2	4872
0.2-0.3	1462
0.3-0.4	620
0.4-0.5	190
0.5-0.6	65
0.6-0.7	20
0.7-0.8	29
0.8-0.85	10
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8163	Intermediate Similarity	NPD66	Approved
0.8163	Intermediate Similarity	NPD64	Approved
0.8163	Intermediate Similarity	NPD8960	Approved
0.8163	Intermediate Similarity	NPD9011	Approved
0.8163	Intermediate Similarity	NPD9008	Approved
0.8163	Intermediate Similarity	NPD72	Approved
0.8163	Intermediate Similarity	NPD65	Approved
0.8163	Intermediate Similarity	NPD9007	Approved
0.8163	Intermediate Similarity	NPD9010	Approved
0.8163	Intermediate Similarity	NPD9009	Approved
0.7708	Intermediate Similarity	NPD9005	Phase 3
0.7708	Intermediate Similarity	NPD9003	Clinical (unspecified phase)
0.7708	Intermediate Similarity	NPD9004	Approved
0.7556	Intermediate Similarity	NPD8599	Approved
0.7556	Intermediate Similarity	NPD8604	Approved
0.7556	Intermediate Similarity	NPD8598	Approved
0.7556	Intermediate Similarity	NPD8600	Approved
0.7556	Intermediate Similarity	NPD8601	Approved
0.7556	Intermediate Similarity	NPD8605	Approved
0.7556	Intermediate Similarity	NPD8603	Approved
0.7556	Intermediate Similarity	NPD8602	Approved
0.7551	Intermediate Similarity	NPD9129	Approved
0.7551	Intermediate Similarity	NPD9126	Approved
0.7551	Intermediate Similarity	NPD71	Approved
0.7547	Intermediate Similarity	NPD73	Approved
0.7407	Intermediate Similarity	NPD8959	Approved
0.7347	Intermediate Similarity	NPD9125	Approved
0.7347	Intermediate Similarity	NPD9123	Approved
0.7347	Intermediate Similarity	NPD9127	Approved
0.7347	Intermediate Similarity	NPD9128	Approved
0.7347	Intermediate Similarity	NPD109	Approved
0.7347	Intermediate Similarity	NPD9130	Phase 3
0.7347	Intermediate Similarity	NPD9121	Approved
0.7347	Intermediate Similarity	NPD9124	Approved
0.7347	Intermediate Similarity	NPD70	Approved
0.7347	Intermediate Similarity	NPD108	Approved
0.7347	Intermediate Similarity	NPD9122	Approved
0.7255	Intermediate Similarity	NPD9002	Approved
0.7255	Intermediate Similarity	NPD9001	Clinical (unspecified phase)
0.6829	Remote Similarity	NPD8618	Approved
0.678	Remote Similarity	NPD8961	Approved
0.6667	Remote Similarity	NPD8202	Approved
0.6667	Remote Similarity	NPD8205	Approved
0.6667	Remote Similarity	NPD8814	Phase 3
0.6585	Remote Similarity	NPD8619	Approved
0.6585	Remote Similarity	NPD8617	Approved
0.6538	Remote Similarity	NPD8964	Approved
0.6429	Remote Similarity	NPD8203	Approved
0.6429	Remote Similarity	NPD54	Approved
0.6429	Remote Similarity	NPD8204	Approved
0.6429	Remote Similarity	NPD8206	Approved
0.6429	Remote Similarity	NPD55	Approved
0.6364	Remote Similarity	NPD8857	Approved
0.6349	Remote Similarity	NPD898	Approved
0.6349	Remote Similarity	NPD896	Approved
0.6349	Remote Similarity	NPD897	Approved
0.6222	Remote Similarity	NPD9053	Approved
0.6222	Remote Similarity	NPD9051	Approved
0.6222	Remote Similarity	NPD9052	Approved
0.5965	Remote Similarity	NPD3728	Approved
0.5965	Remote Similarity	NPD3730	Approved
0.5952	Remote Similarity	NPD8593	Approved
0.5952	Remote Similarity	NPD8549	Clinical (unspecified phase)
0.5952	Remote Similarity	NPD8594	Approved
0.5902	Remote Similarity	NPD9120	Clinical (unspecified phase)
0.5882	Remote Similarity	NPD8975	Clinical (unspecified phase)
0.5873	Remote Similarity	NPD7909	Approved
0.5769	Remote Similarity	NPD8974	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD11	Approved
0.5714	Remote Similarity	NPD376	Approved
0.5686	Remote Similarity	NPD8788	Approved
0.56	Remote Similarity	NPD8995	Clinical (unspecified phase)
0.56	Remote Similarity	NPD8996	Phase 3

Structure

External Identifiers

PubChem CID	439391
ChEMBL	CHEMBL1614745
ZINC

Physicochemical Properties

Molecular Weight:	148.04
ALogP:	-1.3502
MLogP:	1.46
XLogP:	-1.116
# Rotatable Bonds:	7
Polar Surface Area:	94.83
# H-Bond Aceptor:	5
# H-Bond Donor:	3
# Rings:	0
# Heavy Atoms:	10

Download Data

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General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs