NPASS Compound

Structure

NPC471920 OpenBabel07101719152D 43 48 0 0 1 0 0 0 0 0999 V2000 -3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 4.0000 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 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -0.5000 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 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9889 -0.6691 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 6.3986 -3.0827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 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 3.4641 1.0000 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 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 2.5000 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 5.1962 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 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 -0.8660 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3902 -1.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0593 -2.2213 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3956 -1.5827 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 6.8053 -2.1691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4041 -2.9781 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 13 1 0 0 0 0 2 14 1 0 0 0 0 3 35 1 0 0 0 0 4 36 1 0 0 0 0 5 6 2 0 0 0 0 5 15 1 0 0 0 0 6 19 1 0 0 0 0 7 15 2 0 0 0 0 7 22 1 0 0 0 0 8 16 2 0 0 0 0 8 20 1 0 0 0 0 9 17 2 0 0 0 0 9 21 1 0 0 0 0 10 18 1 0 0 0 0 10 37 1 0 0 0 0 11 23 1 0 0 0 0 11 38 1 0 0 0 0 12 39 1 0 0 0 0 12 40 1 0 0 0 0 13 31 2 0 0 0 0 13 41 1 0 0 0 0 14 32 2 0 0 0 0 14 42 1 0 0 0 0 15 24 1 0 0 0 0 16 17 1 0 0 0 0 16 24 1 0 0 0 0 17 27 1 0 0 0 0 18 25 1 0 0 0 0 18 27 2 0 0 0 0 19 22 2 0 0 0 0 19 39 1 0 0 0 0 20 21 2 0 0 0 0 20 35 1 0 0 0 0 21 36 1 0 0 0 0 22 40 1 0 0 0 0 23 28 1 0 0 0 0 23 41 1 6 0 0 0 24 25 2 0 0 0 0 25 29 1 0 0 0 0 26 28 1 0 0 0 0 26 30 1 0 0 0 0 26 33 1 1 0 0 0 27 43 1 0 0 0 0 28 42 1 6 0 0 0 29 34 2 0 0 0 0 29 37 1 0 0 0 0 30 38 1 0 0 0 0 30 43 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	596.15
Volume:	561.369
LogP:	2.974
LogD:	2.307
LogS:	-5.412
# Rotatable Bonds:	9
TPSA:	154.51
# H-Bond Aceptor:	13
# H-Bond Donor:	1
# Rings:	6
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.314
Synthetic Accessibility Score:	4.192
Fsp3:	0.367
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.19
MDCK Permeability:	4.115917545277625e-05
Pgp-inhibitor:	0.852
Pgp-substrate:	0.011
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.001
30% Bioavailability (F30%):	0.124

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.16
Plasma Protein Binding (PPB):	81.55511474609375%
Volume Distribution (VD):	1.217
Pgp-substrate:	6.877796173095703%

ADMET: Metabolism

CYP1A2-inhibitor:	0.215
CYP1A2-substrate:	0.731
CYP2C19-inhibitor:	0.157
CYP2C19-substrate:	0.124
CYP2C9-inhibitor:	0.084
CYP2C9-substrate:	0.84
CYP2D6-inhibitor:	0.891
CYP2D6-substrate:	0.216
CYP3A4-inhibitor:	0.754
CYP3A4-substrate:	0.198

ADMET: Excretion

Clearance (CL):	4.344
Half-life (T1/2):	0.208

ADMET: Toxicity

hERG Blockers:	0.111
Human Hepatotoxicity (H-HT):	0.949
Drug-inuced Liver Injury (DILI):	0.971
AMES Toxicity:	0.836
Rat Oral Acute Toxicity:	0.031
Maximum Recommended Daily Dose:	0.169
Skin Sensitization:	0.045
Carcinogencity:	0.612
Eye Corrosion:	0.003
Eye Irritation:	0.014
Respiratory Toxicity:	0.157

Download Data

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

Natural Product: NPC471920

Natural Product ID:	NPC471920
*Common Name:**	Phyllanthusmins D
IUPAC Name:	[(3S,4R,5R,6S)-4-acetyloxy-6-[[9-(1,3-benzodioxol-5-yl)-6,7-dimethoxy-1-oxo-3H-benzo[f][2]benzofuran-4-yl]oxy]-5-hydroxyoxan-3-yl] acetate
Synonyms:
Standard InCHIKey:	LMBQTGJDJLTHRF-ZCDCQGGYSA-N
Standard InCHI:	InChI=1S/C30H28O13/c1-13(31)41-23-11-38-30(26(33)28(23)42-14(2)32)43-27-17-9-21(36-4)20(35-3)8-16(17)24(25-18(27)10-37-29(25)34)15-5-6-19-22(7-15)40-12-39-19/h5-9,23,26,28,30,33H,10-12H2,1-4H3/t23-,26+,28-,30-/m0/s1
SMILES:	COc1cc2c(O[C@@H]3OC[C@@H]([C@@H]([C@H]3O)OC(=O)C)OC(=O)C)c3COC(=O)c3c(c2cc1OC)c1ccc2c(c1)OCO2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3298727
PubChem CID:	90683253
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0001511] Lignan glycosides

*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
NPO33442	phyllanthus poilanei	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	PMID[24937209]

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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

Activity Type	# Activity
IC50	2
Others	9

Activity Type	# Activity
Cell Line	9
Individual Protein	1
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT139	Cell Line	HT-29	Homo sapiens	IC50	=	170.0	nM	PMID[463041]
NPT1044	Individual Protein	DNA topoisomerase II alpha	Homo sapiens	Activity	=	2.8	%	PMID[463041]
NPT139	Cell Line	HT-29	Homo sapiens	Activity	=	5.51	%	PMID[463041]
NPT139	Cell Line	HT-29	Homo sapiens	Activity	=	7.01	%	PMID[463041]
NPT139	Cell Line	HT-29	Homo sapiens	Activity	=	26.1	%	PMID[463041]
NPT139	Cell Line	HT-29	Homo sapiens	Activity	=	27.3	%	PMID[463041]
NPT139	Cell Line	HT-29	Homo sapiens	Activity	=	28.2	%	PMID[463041]
NPT139	Cell Line	HT-29	Homo sapiens	Activity	=	30.3	%	PMID[463041]
NPT139	Cell Line	HT-29	Homo sapiens	Activity	=	37.5	%	PMID[463041]
NPT139	Cell Line	HT-29	Homo sapiens	Activity	=	38.0	%	PMID[463041]

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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 NPC471920 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	378
0.1-0.2	1594
0.2-0.3	3251
0.3-0.4	8182
0.4-0.5	9692
0.5-0.6	4903
0.6-0.7	6844
0.7-0.8	6863
0.8-0.85	898
0.85-0.9	67
0.9-0.95	9
0.95-1	16

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC20114
1.0	High Similarity	NPC471922
1.0	High Similarity	NPC114550
1.0	High Similarity	NPC471921
1.0	High Similarity	NPC474075

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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 NPC471920 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	323
0.1-0.2	891
0.2-0.3	1650
0.3-0.4	2660
0.4-0.5	1967
0.5-0.6	1059
0.6-0.7	445
0.7-0.8	129
0.8-0.85	26
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8706	High Similarity	NPD5844	Phase 1
0.8667	High Similarity	NPD4967	Phase 2
0.8667	High Similarity	NPD4965	Approved
0.8667	High Similarity	NPD4966	Approved
0.8647	High Similarity	NPD7228	Approved

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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