NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	133.04
Volume:	118.625
LogP:	-3.721
LogD:	-0.79
LogS:	-1.137
# Rotatable Bonds:	3
TPSA:	100.62
# H-Bond Aceptor:	5
# H-Bond Donor:	4
# Rings:	0
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.452
Synthetic Accessibility Score:	2.412
Fsp3:	0.5
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.173
MDCK Permeability:	0.0075979228131473064
Pgp-inhibitor:	0.0
Pgp-substrate:	0.056
Human Intestinal Absorption (HIA):	0.012
20% Bioavailability (F20%):	0.001
30% Bioavailability (F30%):	0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.358
Plasma Protein Binding (PPB):	9.952251434326172%
Volume Distribution (VD):	0.289
Pgp-substrate:	84.22208404541016%

ADMET: Metabolism

CYP1A2-inhibitor:	0.004
CYP1A2-substrate:	0.023
CYP2C19-inhibitor:	0.039
CYP2C19-substrate:	0.042
CYP2C9-inhibitor:	0.013
CYP2C9-substrate:	0.511
CYP2D6-inhibitor:	0.037
CYP2D6-substrate:	0.134
CYP3A4-inhibitor:	0.016
CYP3A4-substrate:	0.006

ADMET: Excretion

Clearance (CL):	9.451
Half-life (T1/2):	0.667

ADMET: Toxicity

hERG Blockers:	0.009
Human Hepatotoxicity (H-HT):	0.085
Drug-inuced Liver Injury (DILI):	0.015
AMES Toxicity:	0.029
Rat Oral Acute Toxicity:	0.031
Maximum Recommended Daily Dose:	0.006
Skin Sensitization:	0.158
Carcinogencity:	0.044
Eye Corrosion:	0.026
Eye Irritation:	0.205
Respiratory Toxicity:	0.086

Download Data

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

Natural Product: NPC285322

Natural Product ID:	NPC285322
*Common Name:**	D-Aspartate
IUPAC Name:	(2R)-2-aminobutanedioic acid
Synonyms:	D-aspartate; D-Aspartic Acid
Standard InCHIKey:	CKLJMWTZIZZHCS-UWTATZPHSA-N
Standard InCHI:	InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)/t2-/m1/s1
SMILES:	OC(=O)C[C@H](C(=O)O)N
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL29757
PubChem CID:	83887
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0000013] Amino acids, peptides, and analogues [CHEMONTID:0000347] Amino acids and derivatives [CHEMONTID:0000060] Alpha amino acids and derivatives [CHEMONTID:0004317] Aspartic acid and derivatives

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
NPO26343	NPC285322	Dried Or Powder	n.a.	1600	n.a.	n.a.	mg/100g	Database [DTU]
NPO26343	NPC285322	Dried Or Powder	n.a.	420	n.a.	n.a.	mg/100g	Database [DTU]
NPO4359	NPC285322	Dried Or Powder	n.a.	42	n.a.	n.a.	mg/100g	Database [DTU]
NPO15810	NPC285322	Dried Or Powder	n.a.	440	n.a.	n.a.	mg/100g	Database [DTU]
NPO8541	NPC285322	Dried Or Powder	n.a.	680	n.a.	n.a.	mg/100g	Database [DTU]
NPO29276	NPC285322	Dried Or Powder	n.a.	1600	n.a.	n.a.	mg/100g	Database [DTU]
NPO27293	NPC285322	No	n.a.	3300	n.a.	n.a.	mg/100g	Database [DTU]
NPO42013	NPC285322	Other	n.a.	1800	n.a.	n.a.	mg/100g	Database [DTU]
NPO18720	NPC285322	Other	n.a.	1300	n.a.	n.a.	mg/100g	Database [DTU]
NPO8541	NPC285322	Other	n.a.	1200	n.a.	n.a.	mg/100g	Database [DTU]
NPO8541	NPC285322	Other	n.a.	71	n.a.	n.a.	mg/100g	Database [DTU]
NPO31303	NPC285322	Puree	n.a.	570	n.a.	n.a.	mg/100g	Database [DTU]
NPO27293	NPC285322	Raw	n.a.	1800	n.a.	n.a.	mg/100g	Database [DTU]
NPO25426	NPC285322	n.a.	n.a.	3200	n.a.	n.a.	mg/100g	Database [DTU]
NPO4359	NPC285322	n.a.	n.a.	990	n.a.	n.a.	mg/100g	Database [DTU]
NPO27293	NPC285322	n.a.	n.a.	1144	n.a.	n.a.	mg/100g	Database [DTU]
NPO16230	NPC285322	n.a.	n.a.	150	n.a.	n.a.	mg/100g	Database [DTU]

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Activity Type	# Activity
EC50	3
IC50	1
Kd	2
Others	1
Potency	10

Activity Type	# Activity
Individual Protein	11
Organism	2
Others	2
Protein Complex	1
SINGLE PROTEIN	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1259	Individual Protein	Metabotropic glutamate receptor 1	Homo sapiens	EC50	>	1000000.0	nM	PMID[558317]
NPT4563	Individual Protein	Metabotropic glutamate receptor 2	Homo sapiens	EC50	>	1000000.0	nM	PMID[558317]
NPT3757	Individual Protein	Metabotropic glutamate receptor 6	Homo sapiens	EC50	>	1000000.0	nM	PMID[558317]
NPT210	Individual Protein	Thyroid stimulating hormone receptor	Homo sapiens	Potency	=	7943.3	nM	PMID[558320]
NPT53	Individual Protein	"4'-phosphopantetheinyl transferase ffp"	Bacillus subtilis	Potency	=	79432.8	nM	PMID[558321]
NPT53	Individual Protein	"4'-phosphopantetheinyl transferase ffp"	Bacillus subtilis	Potency	=	14125.4	nM	PMID[558322]
NPT50	Individual Protein	Tyrosyl-DNA phosphodiesterase 1	Homo sapiens	Potency	n.a.	33498.3	nM	PMID[558323]
NPT49	Individual Protein	DNA-(apurinic or apyrimidinic site) lyase	Homo sapiens	Potency	n.a.	158.5	nM	PMID[558321]
NPT153	Individual Protein	Androgen Receptor	Homo sapiens	Potency	n.a.	26832.5	nM	PubChem BioAssay data set
NPT153	Individual Protein	Androgen Receptor	Homo sapiens	Potency	n.a.	26603.2	nM	PubChem BioAssay data set
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Control	=	58.0	%	PMID[558316]
NPT1496	Protein Complex	Glutamate NMDA receptor	Rattus norvegicus	IC50	=	10000.0	nM	PMID[558318]
NPT23754	SINGLE PROTEIN	Glutamate transporter homolog	Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 /NBRC 100139 / OT-3)	Kd	=	10.0	nM	PMID[558319]
NPT2	Others	Unspecified	""	Kd	=	9.0	nM	PMID[558319]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Potency	n.a.	3380.8	nM	PMID[558322]
NPT2	Others	Unspecified	""	Potency	n.a.	33491.5	nM	PubChem BioAssay data set

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available 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 NPC285322 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	1568
0.1-0.2	31295
0.2-0.3	8329
0.3-0.4	984
0.4-0.5	287
0.5-0.6	115
0.6-0.7	72
0.7-0.8	37
0.8-0.85	8
0.85-0.9	0
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC208793
0.8444	Intermediate Similarity	NPC309658
0.8261	Intermediate Similarity	NPC136159
0.82	Intermediate Similarity	NPC327831
0.814	Intermediate Similarity	NPC66043
0.814	Intermediate Similarity	NPC121517
0.814	Intermediate Similarity	NPC326992
0.814	Intermediate Similarity	NPC168375
0.8085	Intermediate Similarity	NPC153370
0.7778	Intermediate Similarity	NPC167986
0.7778	Intermediate Similarity	NPC291186
0.7736	Intermediate Similarity	NPC93861
0.7736	Intermediate Similarity	NPC43169
0.7736	Intermediate Similarity	NPC112224
0.7736	Intermediate Similarity	NPC327895
0.7727	Intermediate Similarity	NPC237525
0.7727	Intermediate Similarity	NPC326212
0.7708	Intermediate Similarity	NPC227850
0.7619	Intermediate Similarity	NPC116709
0.7619	Intermediate Similarity	NPC272614
0.7619	Intermediate Similarity	NPC21290
0.7609	Intermediate Similarity	NPC132307
0.7609	Intermediate Similarity	NPC126925
0.7609	Intermediate Similarity	NPC325097
0.7447	Intermediate Similarity	NPC329263
0.7447	Intermediate Similarity	NPC118459
0.7447	Intermediate Similarity	NPC327698
0.7442	Intermediate Similarity	NPC63621
0.7333	Intermediate Similarity	NPC53449
0.7321	Intermediate Similarity	NPC322206
0.7317	Intermediate Similarity	NPC114517
0.7308	Intermediate Similarity	NPC60672
0.7308	Intermediate Similarity	NPC322091
0.7292	Intermediate Similarity	NPC136476
0.7292	Intermediate Similarity	NPC49952
0.7143	Intermediate Similarity	NPC316168
0.7059	Intermediate Similarity	NPC315977
0.7059	Intermediate Similarity	NPC137958
0.7059	Intermediate Similarity	NPC273330
0.7059	Intermediate Similarity	NPC125736
0.7	Intermediate Similarity	NPC93081
0.7	Intermediate Similarity	NPC140872
0.6939	Remote Similarity	NPC185755
0.6939	Remote Similarity	NPC213876
0.6889	Remote Similarity	NPC18188
0.6875	Remote Similarity	NPC198301
0.6863	Remote Similarity	NPC324825
0.6863	Remote Similarity	NPC84636
0.6863	Remote Similarity	NPC226027
0.6863	Remote Similarity	NPC193989
0.6863	Remote Similarity	NPC93888
0.6863	Remote Similarity	NPC43204
0.6863	Remote Similarity	NPC316231
0.6863	Remote Similarity	NPC162620
0.6863	Remote Similarity	NPC112890
0.6863	Remote Similarity	NPC152451
0.6863	Remote Similarity	NPC245027
0.6863	Remote Similarity	NPC174246
0.6863	Remote Similarity	NPC62045
0.6863	Remote Similarity	NPC170739
0.6863	Remote Similarity	NPC270805
0.6809	Remote Similarity	NPC219143
0.6809	Remote Similarity	NPC317691
0.6809	Remote Similarity	NPC326808
0.6809	Remote Similarity	NPC226265
0.6809	Remote Similarity	NPC254482
0.6809	Remote Similarity	NPC110533
0.6786	Remote Similarity	NPC190385
0.6727	Remote Similarity	NPC313263
0.6667	Remote Similarity	NPC183845
0.6667	Remote Similarity	NPC279661
0.6604	Remote Similarity	NPC155156
0.6604	Remote Similarity	NPC200550
0.66	Remote Similarity	NPC297220
0.66	Remote Similarity	NPC228932
0.6545	Remote Similarity	NPC2801
0.6545	Remote Similarity	NPC102815
0.6538	Remote Similarity	NPC328378
0.65	Remote Similarity	NPC106216
0.65	Remote Similarity	NPC88898
0.6481	Remote Similarity	NPC317815
0.6481	Remote Similarity	NPC190184
0.6481	Remote Similarity	NPC197087
0.6471	Remote Similarity	NPC181588
0.6471	Remote Similarity	NPC204364
0.6471	Remote Similarity	NPC101249
0.6471	Remote Similarity	NPC118187
0.6444	Remote Similarity	NPC9294
0.6429	Remote Similarity	NPC325985
0.6415	Remote Similarity	NPC114990
0.6364	Remote Similarity	NPC321118
0.6364	Remote Similarity	NPC316889
0.6346	Remote Similarity	NPC318523
0.6341	Remote Similarity	NPC126681
0.6341	Remote Similarity	NPC236709
0.6327	Remote Similarity	NPC276294
0.6275	Remote Similarity	NPC198196
0.625	Remote Similarity	NPC10915
0.6226	Remote Similarity	NPC286989
0.62	Remote Similarity	NPC323974
0.6182	Remote Similarity	NPC329495
0.614	Remote Similarity	NPC38463
0.6102	Remote Similarity	NPC321536
0.6038	Remote Similarity	NPC327542
0.6034	Remote Similarity	NPC278209
0.6	Remote Similarity	NPC143722
0.6	Remote Similarity	NPC177191
0.6	Remote Similarity	NPC107645
0.5965	Remote Similarity	NPC322573
0.5957	Remote Similarity	NPC216443
0.5938	Remote Similarity	NPC196359
0.5938	Remote Similarity	NPC221764
0.5938	Remote Similarity	NPC78312
0.5938	Remote Similarity	NPC135539
0.5932	Remote Similarity	NPC302003
0.5932	Remote Similarity	NPC176164
0.5932	Remote Similarity	NPC189301
0.5932	Remote Similarity	NPC245346
0.5932	Remote Similarity	NPC11433
0.5926	Remote Similarity	NPC17244
0.5902	Remote Similarity	NPC273037
0.5846	Remote Similarity	NPC107224
0.5833	Remote Similarity	NPC254541
0.5833	Remote Similarity	NPC64250
0.5833	Remote Similarity	NPC316826
0.5833	Remote Similarity	NPC317143
0.5833	Remote Similarity	NPC268927
0.5833	Remote Similarity	NPC327748
0.5833	Remote Similarity	NPC321468
0.5833	Remote Similarity	NPC320598
0.5833	Remote Similarity	NPC276928
0.5818	Remote Similarity	NPC319175
0.5806	Remote Similarity	NPC327252
0.5789	Remote Similarity	NPC145235
0.5781	Remote Similarity	NPC470108
0.5769	Remote Similarity	NPC191136
0.5763	Remote Similarity	NPC318260
0.5763	Remote Similarity	NPC317147
0.5738	Remote Similarity	NPC329564
0.5738	Remote Similarity	NPC321419
0.5738	Remote Similarity	NPC68974
0.5738	Remote Similarity	NPC327170
0.5735	Remote Similarity	NPC185084
0.5714	Remote Similarity	NPC289691
0.5692	Remote Similarity	NPC470109
0.5645	Remote Similarity	NPC118429
0.5625	Remote Similarity	NPC69179
0.5625	Remote Similarity	NPC124886
0.5625	Remote Similarity	NPC174304
0.5625	Remote Similarity	NPC50047
0.5625	Remote Similarity	NPC325597
0.5614	Remote Similarity	NPC189178
0.5614	Remote Similarity	NPC263065
0.5606	Remote Similarity	NPC470110

Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC285322 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	916
0.1-0.2	6095
0.2-0.3	1453
0.3-0.4	410
0.4-0.5	152
0.5-0.6	77
0.6-0.7	32
0.7-0.8	12
0.8-0.85	1
0.85-0.9	0
0.9-0.95	1
0.95-1	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD8610	Approved
0.9268	High Similarity	NPD8609	Approved
0.8085	Intermediate Similarity	NPD8614	Approved
0.7778	Intermediate Similarity	NPD8805	Approved
0.7778	Intermediate Similarity	NPD8804	Approved
0.7619	Intermediate Similarity	NPD8211	Approved
0.7619	Intermediate Similarity	NPD8210	Phase 3
0.7609	Intermediate Similarity	NPD8798	Approved
0.7143	Intermediate Similarity	NPD8209	Phase 2
0.7143	Intermediate Similarity	NPD8208	Clinical (unspecified phase)
0.7059	Intermediate Similarity	NPD8872	Phase 3
0.7059	Intermediate Similarity	NPD8871	Approved
0.7	Intermediate Similarity	NPD8808	Approved
0.7	Intermediate Similarity	NPD8809	Approved
0.6939	Remote Similarity	NPD8801	Approved
0.6939	Remote Similarity	NPD8982	Approved
0.6889	Remote Similarity	NPD8623	Phase 1
0.6863	Remote Similarity	NPD9016	Clinical (unspecified phase)
0.6863	Remote Similarity	NPD8803	Clinical (unspecified phase)
0.6863	Remote Similarity	NPD8624	Approved
0.6863	Remote Similarity	NPD9044	Approved
0.6863	Remote Similarity	NPD9021	Approved
0.6863	Remote Similarity	NPD9018	Approved
0.6863	Remote Similarity	NPD9017	Approved
0.6863	Remote Similarity	NPD8802	Approved
0.6809	Remote Similarity	NPD8217	Clinical (unspecified phase)
0.6809	Remote Similarity	NPD8214	Approved
0.6809	Remote Similarity	NPD8216	Approved
0.6809	Remote Similarity	NPD8215	Approved
0.6792	Remote Similarity	NPD8851	Phase 1
0.6786	Remote Similarity	NPD9023	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD8873	Approved
0.6481	Remote Similarity	NPD8849	Clinical (unspecified phase)
0.6481	Remote Similarity	NPD8785	Approved
0.6471	Remote Similarity	NPD8866	Approved
0.6471	Remote Similarity	NPD8867	Approved
0.6471	Remote Similarity	NPD8810	Clinical (unspecified phase)
0.6452	Remote Similarity	NPD1429	Clinical (unspecified phase)
0.6341	Remote Similarity	NPD8594	Approved
0.6341	Remote Similarity	NPD7371	Approved
0.6341	Remote Similarity	NPD8593	Approved
0.6275	Remote Similarity	NPD9020	Approved
0.6207	Remote Similarity	NPD9433	Approved
0.62	Remote Similarity	NPD9019	Approved
0.6111	Remote Similarity	NPD9025	Approved
0.5938	Remote Similarity	NPD8868	Approved
0.5932	Remote Similarity	NPD8865	Approved
0.5926	Remote Similarity	NPD9230	Discontinued
0.5862	Remote Similarity	NPD8979	Approved
0.5862	Remote Similarity	NPD8980	Approved
0.5862	Remote Similarity	NPD8981	Clinical (unspecified phase)
0.5854	Remote Similarity	NPD51	Approved
0.5854	Remote Similarity	NPD7367	Approved
0.5854	Remote Similarity	NPD7368	Approved
0.5849	Remote Similarity	NPD8850	Approved
0.5806	Remote Similarity	NPD575	Clinical (unspecified phase)
0.5789	Remote Similarity	NPD9419	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD1151	Approved
0.569	Remote Similarity	NPD8971	Approved
0.5667	Remote Similarity	NPD8848	Approved
0.5645	Remote Similarity	NPD574	Approved
0.5645	Remote Similarity	NPD9014	Approved
0.5636	Remote Similarity	NPD8946	Approved
0.5636	Remote Similarity	NPD8947	Approved
0.5625	Remote Similarity	NPD348	Approved
0.5614	Remote Similarity	NPD9205	Approved
0.5614	Remote Similarity	NPD9204	Approved
0.561	Remote Similarity	NPD8591	Approved
0.561	Remote Similarity	NPD8592	Approved

Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data