NPASS Compound

Structure

NPC158270 OpenBabel06302216042D 40 45 0 0 1 0 0 0 0 0999 V2000 3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1962 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.9282 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 O 0 0 0 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 -0.0000 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 7 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 39 1 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 5 9 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 11 37 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 39 1 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 15 37 1 0 0 0 0 16 27 2 0 0 0 0 16 17 1 0 0 0 0 17 24 2 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 6 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 6 0 0 0 22 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 25 36 1 0 0 0 0 26 31 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 29 30 1 0 0 0 0 29 34 1 0 0 0 0 30 31 2 0 0 0 0 31 32 1 0 0 0 0 32 33 1 0 0 0 0 34 35 1 0 0 0 0 37 38 1 0 0 0 0 39 40 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	428.07
Volume:	390.0
LogP:	3.315
LogD:	2.033
LogS:	-5.851
# Rotatable Bonds:	5
TPSA:	118.34
# H-Bond Aceptor:	9
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.467
Synthetic Accessibility Score:	3.335
Fsp3:	0.2
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-4.906
MDCK Permeability:	1.1989186532446183e-05
Pgp-inhibitor:	0.263
Pgp-substrate:	0.175
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.001
30% Bioavailability (F30%):	0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.01
Plasma Protein Binding (PPB):	91.37997436523438%
Volume Distribution (VD):	1.281
Pgp-substrate:	4.74297571182251%

ADMET: Metabolism

CYP1A2-inhibitor:	0.808
CYP1A2-substrate:	0.652
CYP2C19-inhibitor:	0.072
CYP2C19-substrate:	0.112
CYP2C9-inhibitor:	0.507
CYP2C9-substrate:	0.935
CYP2D6-inhibitor:	0.51
CYP2D6-substrate:	0.237
CYP3A4-inhibitor:	0.364
CYP3A4-substrate:	0.02

ADMET: Excretion

Clearance (CL):	9.584
Half-life (T1/2):	0.391

ADMET: Toxicity

hERG Blockers:	0.002
Human Hepatotoxicity (H-HT):	0.114
Drug-inuced Liver Injury (DILI):	0.918
AMES Toxicity:	0.654
Rat Oral Acute Toxicity:	0.051
Maximum Recommended Daily Dose:	0.063
Skin Sensitization:	0.548
Carcinogencity:	0.899
Eye Corrosion:	0.01
Eye Irritation:	0.728
Respiratory Toxicity:	0.421

Download Data

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

Natural Product: NPC158270

Natural Product ID:	NPC158270
*Common Name:**	CFZAANHRVVSLNX-LSDHHAIUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CFZAANHRVVSLNX-LSDHHAIUSA-N
Standard InCHI:	InChI=1S/C32H28O8/c1-13-8-21-26(22(33)9-13)32(37)28-18(29(21)34)7-6-17(30(28)35)25-19-10-14(2)40-15(3)24(19)31(36)27-20(25)11-16(38-4)12-23(27)39-5/h6-9,11-12,14-15,33,35-36H,10H2,1-5H3/t14-,15+/m0/s1
SMILES:	Cc1cc2c(c(c1)O)C(=O)c1c(ccc(c3c4C[C@H](C)O[C@H](C)c4c(c4c3cc(cc4OC)OC)O)c1O)C2=O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0001610] Arylnaphthalene lignans

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO20676	Spathelia sorbifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3598592]
NPO17807	Dysosma versipellis	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25712646]
NPO28260	Senna alexandrina	Species	Fabaceae	Eukaryota	n.a.	seed	n.a.	PMID[17345316]
NPO17807	Dysosma versipellis	Species	Berberidaceae	Eukaryota	n.a.	root	n.a.	PMID[17256902]
NPO17807	Dysosma versipellis	Species	Berberidaceae	Eukaryota	Roots	Panan, Zhejiang Province, China	2004-MAY	PMID[17256902]
NPO9402	Morus mongolica	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11429996]
NPO2997	Aloe africana	Species	Xanthorrhoeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7706	Bartlettina karwinskiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2140	Botryococcus braunii	Species	Botryococcaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28260	Senna alexandrina	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
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☑ 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 NPC158270 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	422
0.1-0.2	1648
0.2-0.3	3463
0.3-0.4	9605
0.4-0.5	9228
0.5-0.6	3631
0.6-0.7	5805
0.7-0.8	6334
0.8-0.85	2064
0.85-0.9	448
0.9-0.95	48
0.95-1	1

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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 NPC158270 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	371
0.1-0.2	996
0.2-0.3	1480
0.3-0.4	2664
0.4-0.5	1942
0.5-0.6	1100
0.6-0.7	394
0.7-0.8	163
0.8-0.85	33
0.85-0.9	6
0.9-0.95	1
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
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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