NPASS Compound

Structure

NPC172599 OpenBabel06302216002D 28 32 0 0 1 0 0 0 0 0999 V2000 -0.4067 -2.6456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0933 -1.7796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0933 -1.7796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4067 -0.9135 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4013 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6092 0.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7431 0.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7431 1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6092 2.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4752 1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3412 2.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3412 3.1691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2072 1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2072 0.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3412 0.1691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4752 0.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0733 2.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9393 1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8053 2.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8053 3.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9393 3.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0733 3.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2072 3.6691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2072 4.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7564 3.4781 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.3442 2.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7564 1.8601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 4 2 1 1 0 0 0 4 5 1 0 0 0 0 4 28 1 0 0 0 0 5 6 1 0 0 0 0 6 16 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 7 28 1 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 10 16 1 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 13 14 2 0 0 0 0 13 17 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 17 22 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 19 27 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 25 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	378.11
Volume:	375.299
LogP:	4.631
LogD:	3.283
LogS:	-6.618
# Rotatable Bonds:	3
TPSA:	67.13
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.64
Synthetic Accessibility Score:	3.311
Fsp3:	0.227
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.759
MDCK Permeability:	3.0266006433521397e-05
Pgp-inhibitor:	0.084
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.023
Plasma Protein Binding (PPB):	94.3333740234375%
Volume Distribution (VD):	0.455
Pgp-substrate:	4.285529613494873%

ADMET: Metabolism

CYP1A2-inhibitor:	0.659
CYP1A2-substrate:	0.71
CYP2C19-inhibitor:	0.95
CYP2C19-substrate:	0.092
CYP2C9-inhibitor:	0.863
CYP2C9-substrate:	0.924
CYP2D6-inhibitor:	0.371
CYP2D6-substrate:	0.927
CYP3A4-inhibitor:	0.912
CYP3A4-substrate:	0.215

ADMET: Excretion

Clearance (CL):	10.112
Half-life (T1/2):	0.175

ADMET: Toxicity

hERG Blockers:	0.025
Human Hepatotoxicity (H-HT):	0.71
Drug-inuced Liver Injury (DILI):	0.93
AMES Toxicity:	0.565
Rat Oral Acute Toxicity:	0.548
Maximum Recommended Daily Dose:	0.907
Skin Sensitization:	0.066
Carcinogencity:	0.876
Eye Corrosion:	0.003
Eye Irritation:	0.078
Respiratory Toxicity:	0.901

Download Data

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

Natural Product: NPC172599

Natural Product ID:	NPC172599
*Common Name:**	SXUMBHWIVWENNM-QGZVFWFLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SXUMBHWIVWENNM-QGZVFWFLSA-N
Standard InCHI:	InChI=1S/C22H18O6/c1-11(2)17-7-14-16(28-17)5-4-12-21(23)15(9-25-22(12)14)13-6-19-20(27-10-26-19)8-18(13)24-3/h4-6,8-9,17H,1,7,10H2,2-3H3/t17-/m1/s1
SMILES:	C=C(C)[C@H]1Cc2c(ccc3c(=O)c(coc23)c2cc3c(cc2OC)OCO3)O1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0002901] Isoflav-2-enes [CHEMONTID:0000494] Isoflavones

*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
NPO27819	0nomuraea turkmeniaca	Species	Streptosporangiaceae	Bacteria	n.a.	n.a.	n.a.	PMID[17636954]
NPO26132	Buxus natalensis	Species	Buxaceae	Eukaryota	n.a.	uMhalanga Rocks nature reserve, Durban, South Africa	2007-FEB	PMID[20954721]
NPO26132	Buxus natalensis	Species	Buxaceae	Eukaryota	n.a.	bark	n.a.	PMID[20954721]
NPO27442	Hippeastrum morelianum	Species	Amaryllidaceae	Eukaryota	n.a.	bulb	n.a.	PMID[21105684]
NPO20249	Antheroporum pierrei	Species	Fabaceae	Eukaryota	n.a.	twig	n.a.	PMID[21452840]
NPO20249	Antheroporum pierrei	Species	Fabaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21452840]
NPO27843	Lycoris radiata	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21510636]
NPO27370	Hapsidospora irregularis	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	PMID[28106998]
NPO27843	Lycoris radiata	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28172	Rheum palaestinum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28172	Rheum palaestinum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27843	Lycoris radiata	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27426	Cassytha melantha	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27843	Lycoris radiata	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20929	Patellaria scruposa	Species	Patellariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27442	Hippeastrum morelianum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27426	Cassytha melantha	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27365	Polybia occidentalis	Species	Vespidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28225	Citrus bigaradia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27843	Lycoris radiata	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27268	Cryptocarya densiflora	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27370	Hapsidospora irregularis	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27503	Scombresox saurus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO20249	Antheroporum pierrei	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26132	Buxus natalensis	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27819	0nomuraea turkmeniaca	Species	Streptosporangiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO28022	Baccharis genistifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27720	Bagarius bagarius	Species	Sisoridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27601	Perna canaliculus	Species	Mytilidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28118	Halimeda monile	Species	Halimedaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28172	Rheum palaestinum	Species	Polygonaceae	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 NPC172599 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	532
0.1-0.2	2016
0.2-0.3	4938
0.3-0.4	11116
0.4-0.5	6808
0.5-0.6	4064
0.6-0.7	5843
0.7-0.8	5085
0.8-0.85	1944
0.85-0.9	309
0.9-0.95	39
0.95-1	3

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 NPC172599 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	434
0.1-0.2	1006
0.2-0.3	1922
0.3-0.4	2785
0.4-0.5	1769
0.5-0.6	827
0.6-0.7	273
0.7-0.8	106
0.8-0.85	25
0.85-0.9	3
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