NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	159.05
Volume:	144.661
LogP:	-2.896
LogD:	0.184
LogS:	-0.921
# Rotatable Bonds:	3
TPSA:	100.62
# H-Bond Aceptor:	5
# H-Bond Donor:	4
# Rings:	1
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.496
Synthetic Accessibility Score:	3.678
Fsp3:	0.667
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:	-6.181
MDCK Permeability:	0.006944884546101093
Pgp-inhibitor:	0.0
Pgp-substrate:	0.033
Human Intestinal Absorption (HIA):	0.062
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.708
Plasma Protein Binding (PPB):	9.781045913696289%
Volume Distribution (VD):	0.344
Pgp-substrate:	73.95323181152344%

ADMET: Metabolism

CYP1A2-inhibitor:	0.006
CYP1A2-substrate:	0.026
CYP2C19-inhibitor:	0.036
CYP2C19-substrate:	0.044
CYP2C9-inhibitor:	0.038
CYP2C9-substrate:	0.528
CYP2D6-inhibitor:	0.081
CYP2D6-substrate:	0.121
CYP3A4-inhibitor:	0.017
CYP3A4-substrate:	0.01

ADMET: Excretion

Clearance (CL):	7.826
Half-life (T1/2):	0.708

ADMET: Toxicity

hERG Blockers:	0.012
Human Hepatotoxicity (H-HT):	0.101
Drug-inuced Liver Injury (DILI):	0.036
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.122
Maximum Recommended Daily Dose:	0.008
Skin Sensitization:	0.154
Carcinogencity:	0.036
Eye Corrosion:	0.011
Eye Irritation:	0.19
Respiratory Toxicity:	0.142

Download Data

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

Natural Product: NPC188231

Natural Product ID:	NPC188231
*Common Name:**	(1S,2R)-2-[(S)-Amino(Carboxy)Methyl]Cyclopropane-1-Carboxylic Acid
IUPAC Name:	(1S,2R)-2-[(S)-amino(carboxy)methyl]cyclopropane-1-carboxylic acid
Synonyms:
Standard InCHIKey:	GZOVEPYOCJWRFC-UZBSEBFBSA-N
Standard InCHI:	InChI=1S/C6H9NO4/c7-4(6(10)11)2-1-3(2)5(8)9/h2-4H,1,7H2,(H,8,9)(H,10,11)/t2-,3+,4+/m1/s1
SMILES:	C1[C@H]([C@H]1C(=O)O)[C@@H](C(=O)O)N
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL282842
PubChem CID:	5310958
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:0002404] Alpha amino acids [CHEMONTID:0004146] L-alpha-amino acids

*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
NPO17694	Nicotiana tabacum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11559179]
NPO18777	Endiandra anthropophagorum	Species	Lauraceae	Eukaryota	n.a.	Australian	n.a.	PMID[17583952]
NPO17694	Nicotiana tabacum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18001808]
NPO16051	Beilschmiedia erythrophloia	Species	Lauraceae	Eukaryota	Roots	n.a.	n.a.	PMID[19072217]
NPO18777	Endiandra anthropophagorum	Species	Lauraceae	Eukaryota	n.a.	Australian rainforest	n.a.	PMID[19138858]
NPO17694	Nicotiana tabacum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20954721]
NPO17694	Nicotiana tabacum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23479199]
NPO17694	Nicotiana tabacum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17694	Nicotiana tabacum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17694	Nicotiana tabacum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO17694	Nicotiana tabacum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17364	Engelhardtia chrysolepis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO26440	Cedrela glaziovii	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16051	Beilschmiedia erythrophloia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18503	Eugenia kurzii	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4518.1	Saccharothrix mutabilis subsp. capreolus	Subspecies	Pseudonocardiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO19179	Laminaria ochroleuca	Species	Laminariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15019	Pteridium caudatum	Species	Dennstaedtiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7424	Mitragyna javanica	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12002	Amoora dasyclada	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO9807	Fuscoporia gilva	Species	Hymenochaetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5074	Coryneum modonium	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO12637	Carpinus japonica	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18777	Endiandra anthropophagorum	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13217	Helichrysum cameroonense	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ 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

☑ 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	4
IC50	4
Ki	4
Others	9
Potency	5

Activity Type	# Activity
Individual Protein	3
Organism	1
Others	5
Protein Complex	15
Protein-Protein Interaction	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT48	Individual Protein	Lysine-specific demethylase 4D-like	Homo sapiens	Potency	=	35481.3	nM	PMID[483361]
NPT53	Individual Protein	4'-phosphopantetheinyl transferase ffp	Bacillus subtilis	Potency	=	89125.1	nM	PMID[483361]
NPT3740	Protein Complex	Glutamate receptor ionotropic, kainate	Rattus norvegicus	IC50	=	1600.0	nM	PMID[483356]
NPT3739	Protein Complex	Glutamate receptor ionotropic, AMPA	Rattus norvegicus	IC50	=	600.0	nM	PMID[483356]
NPT1496	Protein Complex	Glutamate NMDA receptor	Rattus norvegicus	IC50	=	5.2	nM	PMID[483356]
NPT35	Others	n.a.		pKa	=	2.5	n.a.	PMID[483357]
NPT35	Others	n.a.		pKa	=	4.6	n.a.	PMID[483357]
NPT35	Others	n.a.		pKa	=	10.0	n.a.	PMID[483357]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Relative potency	=	100.0	n.a.	PMID[483357]
NPT3740	Protein Complex	Glutamate receptor ionotropic, kainate	Rattus norvegicus	Relative potency	=	0.1	n.a.	PMID[483357]
NPT1496	Protein Complex	Glutamate NMDA receptor	Rattus norvegicus	IC50	<	100.0	nM	PMID[483358]
NPT1496	Protein Complex	Glutamate NMDA receptor	Rattus norvegicus	Ki	=	9.0	nM	PMID[483359]
NPT197	Protein-Protein Interaction	Menin/Histone-lysine N-methyltransferase MLL	Homo sapiens	Potency	=	39810.7	nM	PMID[483360]
NPT197	Protein-Protein Interaction	Menin/Histone-lysine N-methyltransferase MLL	Homo sapiens	Potency	=	39810.7	nM	PMID[483361]
NPT95	Individual Protein	Muscarinic acetylcholine receptor M1	Rattus norvegicus	Potency	=	39.8	nM	PMID[483361]
NPT5060	Protein Complex	Ionotropic glutamate receptor NMDA 1/2D	Rattus norvegicus	Ratio	=	1.11	n.a.	PMID[483362]
NPT1839	Protein Complex	Glutamate NMDA receptor; Grin1/Grin2c	Rattus norvegicus	Ratio	=	0.9	n.a.	PMID[483362]
NPT1838	Protein Complex	Glutamate NMDA receptor; Grin1/Grin2b	Rattus norvegicus	Ratio	=	1.23	n.a.	PMID[483362]
NPT1837	Protein Complex	Glutamate NMDA receptor; Grin1/Grin2a	Rattus norvegicus	Ratio	=	0.99	n.a.	PMID[483362]
NPT5060	Protein Complex	Ionotropic glutamate receptor NMDA 1/2D	Rattus norvegicus	EC50	=	36.0	nM	PMID[483362]
NPT1839	Protein Complex	Glutamate NMDA receptor; Grin1/Grin2c	Rattus norvegicus	EC50	=	110.0	nM	PMID[483362]
NPT1838	Protein Complex	Glutamate NMDA receptor; Grin1/Grin2b	Rattus norvegicus	EC50	=	83.0	nM	PMID[483362]
NPT1837	Protein Complex	Glutamate NMDA receptor; Grin1/Grin2a	Rattus norvegicus	EC50	=	262.0	nM	PMID[483362]
NPT1496	Protein Complex	Glutamate NMDA receptor	Rattus norvegicus	Ki	=	6.5	nM	PMID[483362]
NPT2	Others	Unspecified		Ki	=	310.0	nM	PMID[483362]
NPT2	Others	Unspecified		Ki	=	1100.0	nM	PMID[483362]

☑ 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 NPC188231 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	239
0.1-0.2	16574
0.2-0.3	20715
0.3-0.4	4489
0.4-0.5	489
0.5-0.6	139
0.6-0.7	44
0.7-0.8	6
0.8-0.85	0
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	NPC222327
0.8033	Intermediate Similarity	NPC183845
0.8033	Intermediate Similarity	NPC279661
0.7541	Intermediate Similarity	NPC137958
0.7541	Intermediate Similarity	NPC273330
0.7465	Intermediate Similarity	NPC15864
0.7097	Intermediate Similarity	NPC84636
0.7097	Intermediate Similarity	NPC43204
0.7097	Intermediate Similarity	NPC324825
0.7097	Intermediate Similarity	NPC162620
0.7097	Intermediate Similarity	NPC226027
0.7097	Intermediate Similarity	NPC62045
0.7097	Intermediate Similarity	NPC245027
0.7097	Intermediate Similarity	NPC112890
0.7097	Intermediate Similarity	NPC174246
0.7097	Intermediate Similarity	NPC316231
0.7077	Intermediate Similarity	NPC2801
0.6935	Remote Similarity	NPC93081
0.6935	Remote Similarity	NPC140872
0.6875	Remote Similarity	NPC155512
0.6867	Remote Similarity	NPC69374
0.6867	Remote Similarity	NPC90476
0.6812	Remote Similarity	NPC68974
0.6571	Remote Similarity	NPC143722
0.6557	Remote Similarity	NPC323974
0.6522	Remote Similarity	NPC319279
0.6515	Remote Similarity	NPC197087
0.6515	Remote Similarity	NPC190184
0.6494	Remote Similarity	NPC315897
0.6471	Remote Similarity	NPC325985
0.6452	Remote Similarity	NPC118459
0.6452	Remote Similarity	NPC327698
0.6438	Remote Similarity	NPC50047
0.6393	Remote Similarity	NPC276294
0.6377	Remote Similarity	NPC278209
0.6338	Remote Similarity	NPC327170
0.6338	Remote Similarity	NPC329564
0.6301	Remote Similarity	NPC88898
0.6301	Remote Similarity	NPC106216
0.629	Remote Similarity	NPC132307
0.629	Remote Similarity	NPC325097
0.629	Remote Similarity	NPC126925
0.6286	Remote Similarity	NPC190385
0.6286	Remote Similarity	NPC189301
0.6286	Remote Similarity	NPC176164
0.6269	Remote Similarity	NPC263065
0.6269	Remote Similarity	NPC189178
0.625	Remote Similarity	NPC302188
0.6232	Remote Similarity	NPC38463
0.6197	Remote Similarity	NPC317143
0.6197	Remote Similarity	NPC321468
0.6197	Remote Similarity	NPC321536
0.6197	Remote Similarity	NPC276928
0.6197	Remote Similarity	NPC316826
0.6197	Remote Similarity	NPC64250
0.6197	Remote Similarity	NPC327748
0.6197	Remote Similarity	NPC320598
0.6197	Remote Similarity	NPC254541
0.6197	Remote Similarity	NPC268927
0.6196	Remote Similarity	NPC40663
0.619	Remote Similarity	NPC329263
0.6143	Remote Similarity	NPC318260
0.6143	Remote Similarity	NPC317147
0.6133	Remote Similarity	NPC325534
0.6087	Remote Similarity	NPC322573
0.6056	Remote Similarity	NPC245346
0.6056	Remote Similarity	NPC302003
0.6056	Remote Similarity	NPC11433
0.6047	Remote Similarity	NPC320936
0.6	Remote Similarity	NPC101249
0.597	Remote Similarity	NPC50457
0.5957	Remote Similarity	NPC160066
0.5882	Remote Similarity	NPC322946
0.5867	Remote Similarity	NPC289691
0.5844	Remote Similarity	NPC314221
0.5844	Remote Similarity	NPC60424
0.5811	Remote Similarity	NPC118429
0.5806	Remote Similarity	NPC326992
0.5806	Remote Similarity	NPC168375
0.5806	Remote Similarity	NPC121517
0.5789	Remote Similarity	NPC174304
0.5789	Remote Similarity	NPC278881
0.5789	Remote Similarity	NPC325597
0.5738	Remote Similarity	NPC18188
0.5732	Remote Similarity	NPC327272
0.5658	Remote Similarity	NPC226453
0.5658	Remote Similarity	NPC103130
0.5641	Remote Similarity	NPC118524
0.5625	Remote Similarity	NPC291186
0.5625	Remote Similarity	NPC167986

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 NPC188231 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	155
0.1-0.2	4194
0.2-0.3	3707
0.3-0.4	821
0.4-0.5	179
0.5-0.6	65
0.6-0.7	23
0.7-0.8	6
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8209	Intermediate Similarity	NPD9421	Phase 1
0.7541	Intermediate Similarity	NPD8872	Phase 3
0.7541	Intermediate Similarity	NPD8871	Approved
0.7308	Intermediate Similarity	NPD9385	Clinical (unspecified phase)
0.7302	Intermediate Similarity	NPD8851	Phase 1
0.7231	Intermediate Similarity	NPD9454	Approved
0.7215	Intermediate Similarity	NPD9307	Phase 1
0.7097	Intermediate Similarity	NPD9016	Clinical (unspecified phase)
0.7097	Intermediate Similarity	NPD9044	Approved
0.7097	Intermediate Similarity	NPD9017	Approved
0.7097	Intermediate Similarity	NPD9018	Approved
0.7011	Intermediate Similarity	NPD573	Clinical (unspecified phase)
0.6935	Remote Similarity	NPD8808	Approved
0.6935	Remote Similarity	NPD8809	Approved
0.6778	Remote Similarity	NPD842	Phase 3
0.6716	Remote Similarity	NPD8979	Approved
0.6716	Remote Similarity	NPD8980	Approved
0.6716	Remote Similarity	NPD8981	Clinical (unspecified phase)
0.662	Remote Similarity	NPD9676	Phase 3
0.6557	Remote Similarity	NPD9019	Approved
0.6522	Remote Similarity	NPD9438	Approved
0.6522	Remote Similarity	NPD9439	Approved
0.6515	Remote Similarity	NPD8785	Approved
0.6494	Remote Similarity	NPD1825	Clinical (unspecified phase)
0.641	Remote Similarity	NPD9217	Clinical (unspecified phase)
0.6351	Remote Similarity	NPD9201	Clinical (unspecified phase)
0.6329	Remote Similarity	NPD632	Discontinued
0.629	Remote Similarity	NPD8798	Approved
0.6286	Remote Similarity	NPD9023	Clinical (unspecified phase)
0.6286	Remote Similarity	NPD9433	Approved
0.6282	Remote Similarity	NPD1147	Phase 2
0.6269	Remote Similarity	NPD9205	Approved
0.6269	Remote Similarity	NPD9204	Approved
0.625	Remote Similarity	NPD9656	Approved
0.622	Remote Similarity	NPD617	Approved
0.6133	Remote Similarity	NPD8952	Approved
0.6076	Remote Similarity	NPD6944	Clinical (unspecified phase)
0.6056	Remote Similarity	NPD8865	Approved
0.6053	Remote Similarity	NPD375	Phase 2
0.6	Remote Similarity	NPD8866	Approved
0.6	Remote Similarity	NPD8867	Approved
0.5934	Remote Similarity	NPD2682	Approved
0.5882	Remote Similarity	NPD9441	Phase 2
0.5844	Remote Similarity	NPD1429	Clinical (unspecified phase)
0.5821	Remote Similarity	NPD8946	Approved
0.5821	Remote Similarity	NPD8947	Approved
0.5814	Remote Similarity	NPD1125	Discovery
0.5811	Remote Similarity	NPD9014	Approved
0.5802	Remote Similarity	NPD9109	Discontinued
0.5789	Remote Similarity	NPD348	Approved
0.5758	Remote Similarity	NPD8850	Approved
0.5738	Remote Similarity	NPD8623	Phase 1
0.5658	Remote Similarity	NPD9046	Phase 3
0.5658	Remote Similarity	NPD9045	Approved
0.5658	Remote Similarity	NPD9048	Approved
0.5658	Remote Similarity	NPD9047	Approved
0.5641	Remote Similarity	NPD886	Clinical (unspecified phase)
0.5634	Remote Similarity	NPD8971	Approved
0.5625	Remote Similarity	NPD8804	Approved
0.5625	Remote Similarity	NPD8805	Approved
0.5606	Remote Similarity	NPD8801	Approved
0.56	Remote Similarity	NPD574	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