NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	307.08
Volume:	275.211
LogP:	-3.447
LogD:	-1.649
LogS:	-1.235
# Rotatable Bonds:	11
TPSA:	158.82
# H-Bond Aceptor:	9
# H-Bond Donor:	6
# Rings:	0
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.263
Synthetic Accessibility Score:	3.005
Fsp3:	0.6
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.859
MDCK Permeability:	0.0005017935181967914
Pgp-inhibitor:	0.0
Pgp-substrate:	0.03
Human Intestinal Absorption (HIA):	0.117
20% Bioavailability (F20%):	0.475
30% Bioavailability (F30%):	0.061

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.051
Plasma Protein Binding (PPB):	12.51729965209961%
Volume Distribution (VD):	0.34
Pgp-substrate:	85.57475280761719%

ADMET: Metabolism

CYP1A2-inhibitor:	0.001
CYP1A2-substrate:	0.008
CYP2C19-inhibitor:	0.037
CYP2C19-substrate:	0.031
CYP2C9-inhibitor:	0.123
CYP2C9-substrate:	0.451
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.124
CYP3A4-inhibitor:	0.008
CYP3A4-substrate:	0.002

ADMET: Excretion

Clearance (CL):	2.605
Half-life (T1/2):	0.802

ADMET: Toxicity

hERG Blockers:	0.013
Human Hepatotoxicity (H-HT):	0.039
Drug-inuced Liver Injury (DILI):	0.01
AMES Toxicity:	0.85
Rat Oral Acute Toxicity:	0.021
Maximum Recommended Daily Dose:	0.004
Skin Sensitization:	0.209
Carcinogencity:	0.047
Eye Corrosion:	0.003
Eye Irritation:	0.032
Respiratory Toxicity:	0.299

Download Data

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

Natural Product: NPC325597

Natural Product ID:	NPC325597
*Common Name:**	2-Azaniumyl-5-[[1-(Carboxymethylamino)-1-Oxo-3-Sulfanylpropan-2-Yl]Amino]-5-Oxopentanoate
IUPAC Name:	2-azaniumyl-5-[[1-(carboxymethylamino)-1-oxo-3-sulfanylpropan-2-yl]amino]-5-oxopentanoate
Synonyms:
Standard InCHIKey:	RWSXRVCMGQZWBV-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C10H17N3O6S/c11-5(10(18)19)1-2-7(14)13-6(4-20)9(17)12-3-8(15)16/h5-6,20H,1-4,11H2,(H,12,17)(H,13,14)(H,15,16)(H,18,19)
SMILES:	SCC(C(=NCC(=O)O)O)N=C(CCC(C(=O)O)N)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL100476
PubChem CID:	60072620 745
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:0000348] Peptides [CHEMONTID:0004831] Oligopeptides

*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
NPO7925	Asparagus officinalis	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11032480]
NPO7925	Asparagus officinalis	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6821187]
NPO7925	Asparagus officinalis	Species	Asparagaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO7925	Asparagus officinalis	Species	Asparagaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO7925	Asparagus officinalis	Species	Asparagaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO7925	Asparagus officinalis	Species	Asparagaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO7925	Asparagus officinalis	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7925	Asparagus officinalis	Species	Asparagaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO7925	Asparagus officinalis	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO30424	Ostrea rivularis	Species	Ostreidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7925	Asparagus officinalis	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO30109	Ostrea gigas	Species	Ostreidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7925	Asparagus officinalis	Species	Asparagaceae	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
Potency	2

Activity Type	# Activity
Individual Protein	1
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT10	Individual Protein	Geminin	Homo sapiens	Potency	n.a.	20596.2	nM	PMID[470726]
NPT2	Others	Unspecified	""	Potency	n.a.	4466.8	nM	PMID[470726]

☑ 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 NPC325597 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	457
0.1-0.2	27793
0.2-0.3	11998
0.3-0.4	1721
0.4-0.5	401
0.5-0.6	217
0.6-0.7	69
0.7-0.8	27
0.8-0.85	6
0.85-0.9	3
0.9-0.95	2
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC174304
0.9831	High Similarity	NPC289691
0.9206	High Similarity	NPC319046
0.9062	High Similarity	NPC126779
0.8833	High Similarity	NPC321536
0.8689	High Similarity	NPC143722
0.8644	High Similarity	NPC325985
0.8333	Intermediate Similarity	NPC38463
0.8167	Intermediate Similarity	NPC322573
0.8136	Intermediate Similarity	NPC197087
0.8136	Intermediate Similarity	NPC190184
0.8116	Intermediate Similarity	NPC315897
0.7812	Intermediate Similarity	NPC321419
0.7797	Intermediate Similarity	NPC319175
0.7656	Intermediate Similarity	NPC317143
0.7656	Intermediate Similarity	NPC327748
0.7656	Intermediate Similarity	NPC254541
0.7656	Intermediate Similarity	NPC320598
0.7656	Intermediate Similarity	NPC316826
0.7656	Intermediate Similarity	NPC321468
0.7538	Intermediate Similarity	NPC327170
0.7538	Intermediate Similarity	NPC329564
0.75	Intermediate Similarity	NPC189301
0.75	Intermediate Similarity	NPC125736
0.75	Intermediate Similarity	NPC176164
0.7344	Intermediate Similarity	NPC318260
0.7344	Intermediate Similarity	NPC317147
0.7313	Intermediate Similarity	NPC327252
0.7258	Intermediate Similarity	NPC263065
0.7258	Intermediate Similarity	NPC189178
0.7213	Intermediate Similarity	NPC137958
0.7213	Intermediate Similarity	NPC273330
0.7143	Intermediate Similarity	NPC321118
0.7143	Intermediate Similarity	NPC316889
0.7119	Intermediate Similarity	NPC136476
0.7119	Intermediate Similarity	NPC49952
0.7097	Intermediate Similarity	NPC19576
0.7097	Intermediate Similarity	NPC29950
0.7031	Intermediate Similarity	NPC327831
0.6935	Remote Similarity	NPC327239
0.6901	Remote Similarity	NPC118524
0.6833	Remote Similarity	NPC185755
0.6833	Remote Similarity	NPC297220
0.6833	Remote Similarity	NPC306238
0.6833	Remote Similarity	NPC248970
0.6833	Remote Similarity	NPC213876
0.6769	Remote Similarity	NPC2801
0.6667	Remote Similarity	NPC118459
0.6667	Remote Similarity	NPC327698
0.6613	Remote Similarity	NPC140872
0.6613	Remote Similarity	NPC153370
0.6613	Remote Similarity	NPC93081
0.6567	Remote Similarity	NPC278209
0.6562	Remote Similarity	NPC322946
0.6533	Remote Similarity	NPC328457
0.6528	Remote Similarity	NPC325534
0.6508	Remote Similarity	NPC193989
0.6508	Remote Similarity	NPC170739
0.6508	Remote Similarity	NPC112890
0.6508	Remote Similarity	NPC152451
0.6508	Remote Similarity	NPC316231
0.6508	Remote Similarity	NPC324825
0.6508	Remote Similarity	NPC328378
0.6462	Remote Similarity	NPC329495
0.6441	Remote Similarity	NPC317691
0.6441	Remote Similarity	NPC326808
0.6441	Remote Similarity	NPC110533
0.6441	Remote Similarity	NPC254482
0.6406	Remote Similarity	NPC114990
0.6393	Remote Similarity	NPC329263
0.6301	Remote Similarity	NPC470108
0.6286	Remote Similarity	NPC68974
0.6269	Remote Similarity	NPC102815
0.6267	Remote Similarity	NPC472579
0.625	Remote Similarity	NPC43204
0.625	Remote Similarity	NPC315744
0.625	Remote Similarity	NPC84636
0.625	Remote Similarity	NPC62045
0.625	Remote Similarity	NPC226027
0.625	Remote Similarity	NPC174246
0.625	Remote Similarity	NPC245027
0.625	Remote Similarity	NPC162620
0.6216	Remote Similarity	NPC470109
0.6212	Remote Similarity	NPC317815
0.6207	Remote Similarity	NPC193386
0.619	Remote Similarity	NPC204364
0.6154	Remote Similarity	NPC476248
0.6133	Remote Similarity	NPC470110
0.6125	Remote Similarity	NPC59867
0.6119	Remote Similarity	NPC183845
0.6119	Remote Similarity	NPC279661
0.6105	Remote Similarity	NPC72401
0.6105	Remote Similarity	NPC325339
0.6056	Remote Similarity	NPC177191
0.6032	Remote Similarity	NPC228932
0.6032	Remote Similarity	NPC198196
0.6027	Remote Similarity	NPC106216
0.6027	Remote Similarity	NPC88898
0.6026	Remote Similarity	NPC55274
0.6	Remote Similarity	NPC121517
0.6	Remote Similarity	NPC168375
0.6	Remote Similarity	NPC326992
0.5978	Remote Similarity	NPC117829
0.5972	Remote Similarity	NPC118429
0.5957	Remote Similarity	NPC132931
0.5952	Remote Similarity	NPC84128
0.5952	Remote Similarity	NPC53858
0.5946	Remote Similarity	NPC278881
0.5946	Remote Similarity	NPC50047
0.5938	Remote Similarity	NPC118187
0.5873	Remote Similarity	NPC191136
0.5854	Remote Similarity	NPC37681
0.5846	Remote Similarity	NPC227850
0.5846	Remote Similarity	NPC318523
0.5844	Remote Similarity	NPC133183
0.5833	Remote Similarity	NPC314466
0.5833	Remote Similarity	NPC475542
0.5811	Remote Similarity	NPC103130
0.5811	Remote Similarity	NPC226453
0.5811	Remote Similarity	NPC57420
0.5806	Remote Similarity	NPC167986
0.5806	Remote Similarity	NPC291186
0.5806	Remote Similarity	NPC276294
0.5789	Remote Similarity	NPC222327
0.5789	Remote Similarity	NPC188231
0.5775	Remote Similarity	NPC11433
0.5775	Remote Similarity	NPC245346
0.5775	Remote Similarity	NPC302003
0.5769	Remote Similarity	NPC478256
0.5763	Remote Similarity	NPC69179
0.5753	Remote Similarity	NPC477644
0.5714	Remote Similarity	NPC81647
0.5714	Remote Similarity	NPC323974
0.5714	Remote Similarity	NPC126925
0.5714	Remote Similarity	NPC325097
0.5714	Remote Similarity	NPC132307
0.5694	Remote Similarity	NPC268927
0.5694	Remote Similarity	NPC276928
0.5694	Remote Similarity	NPC64250
0.5692	Remote Similarity	NPC136159
0.5672	Remote Similarity	NPC319110
0.5672	Remote Similarity	NPC329181
0.5672	Remote Similarity	NPC50457
0.5667	Remote Similarity	NPC18188
0.5663	Remote Similarity	NPC191774
0.5663	Remote Similarity	NPC314680
0.5658	Remote Similarity	NPC327985
0.5652	Remote Similarity	NPC145235
0.5634	Remote Similarity	NPC283786
0.5632	Remote Similarity	NPC199072
0.5632	Remote Similarity	NPC145748
0.5632	Remote Similarity	NPC95478
0.5632	Remote Similarity	NPC155670
0.5625	Remote Similarity	NPC285322
0.5625	Remote Similarity	NPC208793
0.5604	Remote Similarity	NPC477729
0.56	Remote Similarity	NPC145658

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 NPC325597 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	82
0.1-0.2	5019
0.2-0.3	2997
0.3-0.4	709
0.4-0.5	199
0.5-0.6	88
0.6-0.7	34
0.7-0.8	13
0.8-0.85	2
0.85-0.9	2
0.9-0.95	4
0.95-1	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD348	Approved
0.9355	High Similarity	NPD886	Clinical (unspecified phase)
0.9206	High Similarity	NPD4241	Registered
0.9206	High Similarity	NPD337	Discontinued
0.9062	High Similarity	NPD4242	Approved
0.8788	High Similarity	NPD2262	Clinical (unspecified phase)
0.8667	High Similarity	NPD9433	Approved
0.8136	Intermediate Similarity	NPD8785	Approved
0.8116	Intermediate Similarity	NPD1825	Clinical (unspecified phase)
0.791	Intermediate Similarity	NPD1429	Clinical (unspecified phase)
0.7532	Intermediate Similarity	NPD7643	Phase 1
0.7424	Intermediate Similarity	NPD574	Approved
0.7361	Intermediate Similarity	NPD6944	Clinical (unspecified phase)
0.7313	Intermediate Similarity	NPD575	Clinical (unspecified phase)
0.7258	Intermediate Similarity	NPD9205	Approved
0.7258	Intermediate Similarity	NPD9204	Approved
0.7213	Intermediate Similarity	NPD8871	Approved
0.7213	Intermediate Similarity	NPD8872	Phase 3
0.7213	Intermediate Similarity	NPD329	Discontinued
0.7097	Intermediate Similarity	NPD61	Approved
0.7097	Intermediate Similarity	NPD8847	Approved
0.7097	Intermediate Similarity	NPD8846	Approved
0.6984	Remote Similarity	NPD8851	Phase 1
0.6892	Remote Similarity	NPD1147	Phase 2
0.6833	Remote Similarity	NPD8870	Approved
0.6833	Remote Similarity	NPD8982	Approved
0.679	Remote Similarity	NPD3733	Clinical (unspecified phase)
0.6613	Remote Similarity	NPD9214	Phase 3
0.6613	Remote Similarity	NPD8614	Approved
0.6613	Remote Similarity	NPD8808	Approved
0.6613	Remote Similarity	NPD8809	Approved
0.6613	Remote Similarity	NPD9213	Approved
0.6579	Remote Similarity	NPD366	Approved
0.6575	Remote Similarity	NPD9452	Clinical (unspecified phase)
0.6562	Remote Similarity	NPD9441	Phase 2
0.6528	Remote Similarity	NPD8952	Approved
0.6508	Remote Similarity	NPD9021	Approved
0.6508	Remote Similarity	NPD8802	Approved
0.6508	Remote Similarity	NPD9044	Approved
0.6508	Remote Similarity	NPD8803	Clinical (unspecified phase)
0.65	Remote Similarity	NPD8869	Approved
0.6441	Remote Similarity	NPD8215	Approved
0.6441	Remote Similarity	NPD8214	Approved
0.6374	Remote Similarity	NPD842	Phase 3
0.6351	Remote Similarity	NPD9451	Clinical (unspecified phase)
0.6349	Remote Similarity	NPD8873	Approved
0.629	Remote Similarity	NPD8801	Approved
0.625	Remote Similarity	NPD9017	Approved
0.625	Remote Similarity	NPD9018	Approved
0.625	Remote Similarity	NPD9016	Clinical (unspecified phase)
0.625	Remote Similarity	NPD364	Discontinued
0.6212	Remote Similarity	NPD8849	Clinical (unspecified phase)
0.6212	Remote Similarity	NPD9386	Approved
0.6212	Remote Similarity	NPD9420	Clinical (unspecified phase)
0.619	Remote Similarity	NPD9577	Approved
0.618	Remote Similarity	NPD1749	Approved
0.6145	Remote Similarity	NPD1125	Discovery
0.6129	Remote Similarity	NPD397	Phase 2
0.6049	Remote Similarity	NPD3160	Suspended
0.6032	Remote Similarity	NPD9020	Approved
0.6	Remote Similarity	NPD9421	Phase 1
0.5972	Remote Similarity	NPD9014	Approved
0.5909	Remote Similarity	NPD9025	Approved
0.5873	Remote Similarity	NPD9658	Clinical (unspecified phase)
0.5862	Remote Similarity	NPD7760	Phase 2
0.5862	Remote Similarity	NPD7759	Phase 2
0.5844	Remote Similarity	NPD1815	Discontinued
0.5811	Remote Similarity	NPD9047	Approved
0.5811	Remote Similarity	NPD9046	Phase 3
0.5811	Remote Similarity	NPD9045	Approved
0.5811	Remote Similarity	NPD9048	Approved
0.5806	Remote Similarity	NPD8805	Approved
0.5806	Remote Similarity	NPD8804	Approved
0.5789	Remote Similarity	NPD9232	Phase 2
0.5789	Remote Similarity	NPD9233	Phase 3
0.5789	Remote Similarity	NPD9231	Phase 3
0.5789	Remote Similarity	NPD8842	Clinical (unspecified phase)
0.5789	Remote Similarity	NPD2263	Discontinued
0.5783	Remote Similarity	NPD4815	Discontinued
0.5775	Remote Similarity	NPD8865	Approved
0.5714	Remote Similarity	NPD8980	Approved
0.5714	Remote Similarity	NPD8979	Approved
0.5714	Remote Similarity	NPD9019	Approved
0.5714	Remote Similarity	NPD5792	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD8798	Approved
0.5714	Remote Similarity	NPD8981	Clinical (unspecified phase)
0.5699	Remote Similarity	NPD573	Clinical (unspecified phase)
0.5698	Remote Similarity	NPD4829	Discontinued
0.5667	Remote Similarity	NPD8623	Phase 1
0.5663	Remote Similarity	NPD4278	Clinical (unspecified phase)
0.5652	Remote Similarity	NPD9419	Clinical (unspecified phase)
0.5641	Remote Similarity	NPD3724	Clinical (unspecified phase)
0.5632	Remote Similarity	NPD326	Approved
0.5625	Remote Similarity	NPD8610	Approved
0.5616	Remote Similarity	NPD902	Approved
0.5606	Remote Similarity	NPD8577	Discontinued

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