NPASS Compound

Structure

CID150879 OpenBabel06191715522D 28 32 0 0 1 0 0 0 0 0999 V2000 4.3301 -4.5000 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 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4049 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8171 -0.1910 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 1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8171 -1.8090 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 3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 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 3.4641 -3.0000 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 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 -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 2 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 0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 N 0 0 3 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 4.3301 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 26 1 0 0 0 0 2 27 1 0 0 0 0 3 28 1 0 0 0 0 4 5 1 0 0 0 0 4 8 1 0 0 0 0 5 19 1 0 0 0 0 6 7 2 0 0 0 0 6 13 1 0 0 0 0 7 14 1 0 0 0 0 8 24 1 0 0 0 0 9 13 2 0 0 0 0 9 15 1 0 0 0 0 10 16 2 0 0 0 0 10 20 1 0 0 0 0 11 17 2 0 0 0 0 11 21 1 0 0 0 0 12 18 1 0 0 0 0 12 24 1 0 0 0 0 13 26 1 0 0 0 0 14 15 2 0 0 0 0 14 18 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 22 1 0 0 0 0 18 22 2 0 0 0 0 19 23 1 0 0 0 0 19 24 1 6 0 0 0 20 21 2 0 0 0 0 20 27 1 0 0 0 0 21 28 1 0 0 0 0 22 23 1 0 0 0 0 23 25 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	379.18
Volume:	391.284
LogP:	3.724
LogD:	3.22
LogS:	-4.791
# Rotatable Bonds:	3
TPSA:	51.16
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.697
Synthetic Accessibility Score:	3.264
Fsp3:	0.391
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-5.112
MDCK Permeability:	3.434860991546884e-05
Pgp-inhibitor:	0.932
Pgp-substrate:	0.996
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.011
30% Bioavailability (F30%):	0.254

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.981
Plasma Protein Binding (PPB):	79.23069763183594%
Volume Distribution (VD):	1.946
Pgp-substrate:	8.139331817626953%

ADMET: Metabolism

CYP1A2-inhibitor:	0.405
CYP1A2-substrate:	0.97
CYP2C19-inhibitor:	0.061
CYP2C19-substrate:	0.941
CYP2C9-inhibitor:	0.007
CYP2C9-substrate:	0.737
CYP2D6-inhibitor:	0.961
CYP2D6-substrate:	0.918
CYP3A4-inhibitor:	0.019
CYP3A4-substrate:	0.801

ADMET: Excretion

Clearance (CL):	8.167
Half-life (T1/2):	0.277

ADMET: Toxicity

hERG Blockers:	0.439
Human Hepatotoxicity (H-HT):	0.461
Drug-inuced Liver Injury (DILI):	0.945
AMES Toxicity:	0.812
Rat Oral Acute Toxicity:	0.445
Maximum Recommended Daily Dose:	0.889
Skin Sensitization:	0.825
Carcinogencity:	0.068
Eye Corrosion:	0.003
Eye Irritation:	0.018
Respiratory Toxicity:	0.942

Download Data

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

Natural Product: NPC150879

Natural Product ID:	NPC150879
*Common Name:**	(13Ar,14R)-2,3,6-Trimethoxy-9,11,12,13,13A,14-Hexahydrophenanthro[9,10-F]Indolizin-14-Ol
IUPAC Name:	(13aR,14R)-2,3,6-trimethoxy-9,11,12,13,13a,14-hexahydrophenanthro[9,10-f]indolizin-14-ol
Synonyms:
Standard InCHIKey:	VEPWWLXWVFFRLY-XXBNENTESA-N
Standard InCHI:	InChI=1S/C23H25NO4/c1-26-13-6-7-14-15(9-13)16-10-20(27-2)21(28-3)11-17(16)22-18(14)12-24-8-4-5-19(24)23(22)25/h6-7,9-11,19,23,25H,4-5,8,12H2,1-3H3/t19-,23+/m1/s1
SMILES:	COc1ccc2c(c1)c1cc(OC)c(cc1c1c2CN2CCC[C@@H]2[C@@H]1O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1958058
PubChem CID:	46183346
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000025] Phenanthrenes and derivatives [CHEMONTID:0001906] Phenanthroindolizidines

*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
NPO28410	Nandina domestica	Species	Berberidaceae	Eukaryota	n.a.	fruit	n.a.	PMID[24897106]
NPO28410	Nandina domestica	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22029392]
NPO18515	Uncaria pilosa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14290	Bryonia cretica	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17803	Parmelia omphalodes	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24981	Dimetia capitellata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28410	Nandina domestica	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18056	Silene rubicunda	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18788	Isertia hypoleuca	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24981	Dimetia capitellata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]

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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
GI50	2
Others	8

Activity Type	# Activity
Cell Line	2
Organism	8

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT786	Organism	Tobacco mosaic virus	Tobacco mosaic virus	Activity	=	7.3	%	PMID[530807]
NPT786	Organism	Tobacco mosaic virus	Tobacco mosaic virus	Activity	=	39.6	%	PMID[530807]
NPT786	Organism	Tobacco mosaic virus	Tobacco mosaic virus	Activity	=	10.2	%	PMID[530807]
NPT786	Organism	Tobacco mosaic virus	Tobacco mosaic virus	Activity	=	34.9	%	PMID[530807]
NPT786	Organism	Tobacco mosaic virus	Tobacco mosaic virus	Activity	=	14.2	%	PMID[530807]
NPT786	Organism	Tobacco mosaic virus	Tobacco mosaic virus	Activity	=	38.5	%	PMID[530807]
NPT786	Organism	Tobacco mosaic virus	Tobacco mosaic virus	Inhibition	=	21.6	%	PMID[530807]
NPT786	Organism	Tobacco mosaic virus	Tobacco mosaic virus	Inhibition	=	43.5	%	PMID[530807]
NPT81	Cell Line	A549	Homo sapiens	GI50	>	10000.0	nM	PMID[530806]
NPT116	Cell Line	HL-60	Homo sapiens	GI50	>	10000.0	nM	PMID[530806]

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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 NPC150879 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	288
0.1-0.2	1334
0.2-0.3	4509
0.3-0.4	12683
0.4-0.5	5649
0.5-0.6	12633
0.6-0.7	4535
0.7-0.8	756
0.8-0.85	250
0.85-0.9	46
0.9-0.95	7
0.95-1	7

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Similarity Score	Similarity Level	Natural Product ID
0.9805	High Similarity	NPC233650
0.9742	High Similarity	NPC134858
0.9618	High Similarity	NPC210140
0.949	High Similarity	NPC169743
0.9167	High Similarity	NPC244112

Showing 1 to 5 of 200 entries

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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 NPC150879 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	176
0.1-0.2	647
0.2-0.3	890
0.3-0.4	2006
0.4-0.5	2594
0.5-0.6	1859
0.6-0.7	781
0.7-0.8	178
0.8-0.85	18
0.85-0.9	1
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8868	High Similarity	NPD6818	Clinical (unspecified phase)
0.8485	Intermediate Similarity	NPD7201	Clinical (unspecified phase)
0.8452	Intermediate Similarity	NPD4664	Clinical (unspecified phase)
0.8408	Intermediate Similarity	NPD5241	Discontinued
0.8383	Intermediate Similarity	NPD3051	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