NPASS Compound

Structure

NPC110103 OpenBabel06302215082D 21 24 0 0 1 0 0 0 0 0999 V2000 0.5262 2.4620 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8468 1.5172 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0107 1.0072 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8823 1.4926 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7204 0.9891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7098 -0.0181 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7356 -0.0290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7249 -1.0365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6991 -1.0257 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 -1.6884 -2.0324 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8402 -2.4832 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0213 -2.0143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8985 -2.5085 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7651 -1.9959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7544 -0.9891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8772 -0.4949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0107 -1.0076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8612 -0.5042 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6136 -0.4808 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6349 -2.4858 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 3 2 1 6 0 0 0 3 4 1 0 0 0 0 3 19 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 18 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 18 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 17 2 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 14 21 1 0 0 0 0 15 16 2 0 0 0 0 15 20 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	285.14
Volume:	292.548
LogP:	1.529
LogD:	1.847
LogS:	-1.706
# Rotatable Bonds:	1
TPSA:	52.93
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.776
Synthetic Accessibility Score:	4.679
Fsp3:	0.412
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.914
MDCK Permeability:	2.233344093838241e-05
Pgp-inhibitor:	0.822
Pgp-substrate:	0.729
Human Intestinal Absorption (HIA):	0.119
20% Bioavailability (F20%):	0.896
30% Bioavailability (F30%):	0.017

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.995
Plasma Protein Binding (PPB):	69.3282699584961%
Volume Distribution (VD):	2.367
Pgp-substrate:	21.599946975708008%

ADMET: Metabolism

CYP1A2-inhibitor:	0.025
CYP1A2-substrate:	0.27
CYP2C19-inhibitor:	0.053
CYP2C19-substrate:	0.808
CYP2C9-inhibitor:	0.334
CYP2C9-substrate:	0.867
CYP2D6-inhibitor:	0.118
CYP2D6-substrate:	0.491
CYP3A4-inhibitor:	0.444
CYP3A4-substrate:	0.924

ADMET: Excretion

Clearance (CL):	21.187
Half-life (T1/2):	0.852

ADMET: Toxicity

hERG Blockers:	0.441
Human Hepatotoxicity (H-HT):	0.529
Drug-inuced Liver Injury (DILI):	0.075
AMES Toxicity:	0.749
Rat Oral Acute Toxicity:	0.076
Maximum Recommended Daily Dose:	0.953
Skin Sensitization:	0.929
Carcinogencity:	0.854
Eye Corrosion:	0.003
Eye Irritation:	0.016
Respiratory Toxicity:	0.615

Download Data

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

Natural Product: NPC110103

Natural Product ID:	NPC110103
*Common Name:**	GNBQGLMYBIWCOO-CWQZNGJJSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GNBQGLMYBIWCOO-CWQZNGJJSA-N
Standard InCHI:	InChI=1S/C17H19NO3/c1-21-13-3-2-12-5-7-18-6-4-11-8-15(19)16(20)9-14(11)17(12,18)10-13/h2-3,5,8-9,13,19-20H,4,6-7,10H2,1H3/t13-,17?/m0/s1
SMILES:	CO[C@H]1C=CC2=CCN3CCc4cc(c(cc4C23C1)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	3048724
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0001782] Erythrina alkaloids [CHEMONTID:0002780] Erythrinanes

*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
NPO14905	Erythrina variegata	Species	Fabaceae	Eukaryota	n.a.	root	n.a.	PMID[10869220]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	stem bark	n.a.	n.a.	PMID[17489632]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	stem	n.a.	PMID[18484536]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	stem bark	Mukono, Uganda	2005-JUN	PMID[19008110]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19836230]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20337486]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21116437]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14905	Erythrina variegata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17657	Erythrina arborescens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17657	Erythrina arborescens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10227	Erythrina lithosperma	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16399	Erythrina folkersii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14905	Erythrina variegata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20680	Erythrina melanacantha	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28361	Erythrina salviiflora	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10227	Erythrina lithosperma	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14905	Erythrina variegata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO30554	Erythrina folkersll	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29998	Erythrina salvllflora	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20680	Erythrina melanacantha	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO17657	Erythrina arborescens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10227	Erythrina lithosperma	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14905	Erythrina variegata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17657	Erythrina arborescens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20680	Erythrina melanacantha	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28361	Erythrina salviiflora	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16399	Erythrina folkersii	Species	Fabaceae	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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC110103 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	222
0.1-0.2	1317
0.2-0.3	5483
0.3-0.4	12194
0.4-0.5	8790
0.5-0.6	11120
0.6-0.7	2900
0.7-0.8	543
0.8-0.85	100
0.85-0.9	24
0.9-0.95	4
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID

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 NPC110103 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	152
0.1-0.2	677
0.2-0.3	897
0.3-0.4	1952
0.4-0.5	2892
0.5-0.6	1800
0.6-0.7	645
0.7-0.8	127
0.8-0.85	8
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

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