NPASS Compound

Structure

CID10908 OpenBabel06191715342D 46 52 0 0 1 0 0 0 0 0999 V2000 2.3291 -4.1877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3783 -0.7232 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6386 -4.2423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3291 1.6788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9525 1.6162 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7351 1.9402 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1507 -4.5450 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0113 -4.0828 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5542 -1.5438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7381 -4.6211 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6793 -4.1420 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9081 -2.4373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1759 -1.7433 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0221 0.8866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1759 -2.7211 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6014 0.5059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1541 -3.3317 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3661 -1.0457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5874 -2.3952 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3291 -0.2767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1024 0.9862 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6356 -1.2545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6454 -3.8026 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5894 -1.7020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3291 -1.2545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4027 0.5753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3518 -3.9737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4824 -1.7433 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4824 -2.7211 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.9418 -0.4975 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3113 -3.1905 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4824 0.2122 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3605 -3.0503 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6356 -0.2767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5965 0.9316 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3626 -0.1167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3908 0.4662 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6910 0.0553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3291 -3.2100 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.5612 -0.1862 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.6714 -4.0996 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4824 1.1899 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0196 1.7211 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5813 0.3613 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9332 -3.5961 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 39 1 0 0 0 0 2 40 1 0 0 0 0 3 41 1 0 0 0 0 4 42 1 0 0 0 0 5 43 1 0 0 0 0 6 44 1 0 0 0 0 7 10 1 0 0 0 0 7 23 2 0 0 0 0 8 11 2 0 0 0 0 8 23 1 0 0 0 0 9 12 2 0 0 0 0 9 24 1 0 0 0 0 10 27 2 0 0 0 0 11 27 1 0 0 0 0 12 31 1 0 0 0 0 13 15 1 0 0 0 0 13 25 1 0 0 0 0 14 16 1 0 0 0 0 14 26 1 0 0 0 0 15 39 1 0 0 0 0 16 40 1 0 0 0 0 17 23 1 0 0 0 0 18 24 1 0 0 0 0 19 24 2 0 0 0 0 19 33 1 0 0 0 0 20 25 2 0 0 0 0 20 32 1 0 0 0 0 21 26 2 0 0 0 0 21 35 1 0 0 0 0 22 28 2 0 0 0 0 22 34 1 0 0 0 0 25 28 1 0 0 0 0 26 36 1 0 0 0 0 27 45 1 0 0 0 0 28 29 1 0 0 0 0 29 17 1 6 0 0 0 29 39 1 0 0 0 0 30 18 1 6 0 0 0 30 36 1 0 0 0 0 30 40 1 0 0 0 0 31 33 2 0 0 0 0 31 41 1 0 0 0 0 32 34 2 0 0 0 0 32 42 1 0 0 0 0 33 45 1 0 0 0 0 34 46 1 0 0 0 0 35 37 2 0 0 0 0 35 43 1 0 0 0 0 36 38 2 0 0 0 0 37 38 1 0 0 0 0 37 44 1 0 0 0 0 38 46 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	622.3
Volume:	649.006
LogP:	6.34
LogD:	4.054
LogS:	-6.034
# Rotatable Bonds:	4
TPSA:	61.86
# H-Bond Aceptor:	8
# H-Bond Donor:	0
# Rings:	8
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.238
Synthetic Accessibility Score:	5.725
Fsp3:	0.368
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected
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:	-5.796
MDCK Permeability:	2.740371746767778e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.974
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.41
30% Bioavailability (F30%):	0.947

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.223
Plasma Protein Binding (PPB):	64.35213470458984%
Volume Distribution (VD):	1.011
Pgp-substrate:	18.79802703857422%

ADMET: Metabolism

CYP1A2-inhibitor:	0.049
CYP1A2-substrate:	0.972
CYP2C19-inhibitor:	0.077
CYP2C19-substrate:	0.977
CYP2C9-inhibitor:	0.047
CYP2C9-substrate:	0.647
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.961
CYP3A4-inhibitor:	0.142
CYP3A4-substrate:	0.959

ADMET: Excretion

Clearance (CL):	9.781
Half-life (T1/2):	0.208

ADMET: Toxicity

hERG Blockers:	0.98
Human Hepatotoxicity (H-HT):	0.039
Drug-inuced Liver Injury (DILI):	0.746
AMES Toxicity:	0.086
Rat Oral Acute Toxicity:	0.458
Maximum Recommended Daily Dose:	0.993
Skin Sensitization:	0.455
Carcinogencity:	0.035
Eye Corrosion:	0.003
Eye Irritation:	0.004
Respiratory Toxicity:	0.4

Download Data

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

Natural Product: NPC10908

Natural Product ID:	NPC10908
*Common Name:**	Isotetrandrine
IUPAC Name:	n.a.
Synonyms:	NSC-97338
Standard InCHIKey:	WVTKBKWTSCPRNU-IHLOFXLRSA-N
Standard InCHI:	InChI=1S/C38H42N2O6/c1-39-15-13-25-20-32(42-4)34-22-28(25)29(39)17-23-7-10-27(11-8-23)45-33-19-24(9-12-31(33)41-3)18-30-36-26(14-16-40(30)2)21-35(43-5)37(44-6)38(36)46-34/h7-12,19-22,29-30H,13-18H2,1-6H3/t29-,30+/m1/s1
SMILES:	CN1CCc2cc(c3cc2[C@H]1Cc1ccc(cc1)Oc1cc(ccc1OC)C[C@H]1c2c(CCN1C)cc(c(c2O3)OC)OC)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL504757
PubChem CID:	5351212
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds

*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
NPO3849	Cyclea barbata	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9917283]
NPO33281	pseuhxandra sclerocarpa	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[8676127]
NPO3849	Cyclea barbata	Species	Menispermaceae	Eukaryota	roots	n.a.	n.a.	PMID[8450318]
NPO3849	Cyclea barbata	Species	Menispermaceae	Eukaryota	roots	n.a.	n.a.	PMID[8289066]
NPO21435	Thalictrum faberi	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7528786]
NPO12773	Stephania tetrandra	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3728032]
NPO3148	Melianthus major	Species	Melianthaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[32663024]
NPO31374	Stephania cepharantha	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32129063]
NPO12588	Cornus officinalis	Species	Cornaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[29140705]
NPO16121	Pestalotiopsis disseminata	Species	Sporocadaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26641923]

Showing 1 to 10 of 126 entries

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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	58
IC50	3
Others	35

Activity Type	# Activity
Cell Line	63
Individual Protein	3
Organism	24
Others	6

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20	Organism	Candida albicans	Candida albicans	MIC80	=	64.0	ug.mL-1	PMID[510400]
NPT378	Cell Line	NCI/ADR-RES	Homo sapiens	TGI	=	58.0	%	PMID[510399]
NPT2	Others	Unspecified		FC	=	20.0	n.a.	PMID[510399]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	AUC	=	6279.0	ug/hr/L	PMID[510399]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Cmax	=	0.237	ug.mL-1	PMID[510399]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Tmax	=	6.0	hr	PMID[510399]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	T1/2	=	20.0	hr	PMID[510399]
NPT605	Organism	Homo sapiens	Homo sapiens	AUC	=	192.0	ng/ml	PMID[510399]
NPT605	Organism	Homo sapiens	Homo sapiens	T1/2	=	120.0	hr	PMID[510399]
NPT2	Others	Unspecified		TGI	=	62.0	%	PMID[510399]

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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 NPC10908 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	434
0.1-0.2	2015
0.2-0.3	10197
0.3-0.4	8089
0.4-0.5	6310
0.5-0.6	10195
0.6-0.7	4499
0.7-0.8	707
0.8-0.85	118
0.85-0.9	41
0.9-0.95	40
0.95-1	52

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC317145
1.0	High Similarity	NPC227060
1.0	High Similarity	NPC198498
1.0	High Similarity	NPC76682
1.0	High Similarity	NPC115284

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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 NPC10908 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	231
0.1-0.2	848
0.2-0.3	1112
0.3-0.4	2288
0.4-0.5	2384
0.5-0.6	1564
0.6-0.7	595
0.7-0.8	115
0.8-0.85	4
0.85-0.9	3
0.9-0.95	1
0.95-1	5

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD8252	Approved
1.0	High Similarity	NPD8251	Approved
1.0	High Similarity	NPD8099	Discontinued
0.9937	High Similarity	NPD8156	Discontinued
0.9573	High Similarity	NPD8054	Approved

Showing 1 to 5 of 200 entries

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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