NPASS Compound

Structure

CID311256 OpenBabel06191716122D 27 29 0 0 1 0 0 0 0 0999 V2000 -6.0622 2.5000 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 -3.4641 -0.0000 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 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 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 -1.2321 3.8660 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 -0.8660 1.5000 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 -2.5981 2.5000 0.0000 C 0 0 2 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 -0.8660 -0.5000 0.0000 C 0 0 0 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 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 C 0 0 1 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 -0.2321 3.8660 0.0000 O 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 -0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2321 3.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 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 4 2 0 0 0 0 3 11 1 0 0 0 0 4 15 1 0 0 0 0 5 11 2 0 0 0 0 5 17 1 0 0 0 0 6 12 2 0 0 0 0 6 18 1 0 0 0 0 7 13 2 0 0 0 0 7 16 1 0 0 0 0 8 12 1 0 0 0 0 8 20 1 0 0 0 0 9 14 1 0 0 0 0 9 21 1 0 0 0 0 10 20 1 0 0 0 0 10 22 1 0 0 0 0 12 13 1 0 0 0 0 13 19 1 0 0 0 0 14 19 1 0 0 0 0 14 20 1 1 0 0 0 15 17 2 0 0 0 0 15 23 1 0 0 0 0 16 18 2 0 0 0 0 16 24 1 0 0 0 0 17 26 1 0 0 0 0 18 27 1 0 0 0 0 19 11 1 6 0 0 0 20 25 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	376.15
Volume:	374.52
LogP:	0.961
LogD:	1.369
LogS:	-2.183
# Rotatable Bonds:	5
TPSA:	119.61
# H-Bond Aceptor:	7
# H-Bond Donor:	5
# Rings:	3
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.531
Synthetic Accessibility Score:	3.787
Fsp3:	0.4
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.37
MDCK Permeability:	4.118064680369571e-05
Pgp-inhibitor:	0.003
Pgp-substrate:	0.993
Human Intestinal Absorption (HIA):	0.119
20% Bioavailability (F20%):	0.343
30% Bioavailability (F30%):	0.118

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.237
Plasma Protein Binding (PPB):	93.89234924316406%
Volume Distribution (VD):	0.963
Pgp-substrate:	8.68431568145752%

ADMET: Metabolism

CYP1A2-inhibitor:	0.038
CYP1A2-substrate:	0.796
CYP2C19-inhibitor:	0.018
CYP2C19-substrate:	0.504
CYP2C9-inhibitor:	0.031
CYP2C9-substrate:	0.669
CYP2D6-inhibitor:	0.05
CYP2D6-substrate:	0.619
CYP3A4-inhibitor:	0.333
CYP3A4-substrate:	0.726

ADMET: Excretion

Clearance (CL):	13.762
Half-life (T1/2):	0.727

ADMET: Toxicity

hERG Blockers:	0.046
Human Hepatotoxicity (H-HT):	0.413
Drug-inuced Liver Injury (DILI):	0.21
AMES Toxicity:	0.108
Rat Oral Acute Toxicity:	0.103
Maximum Recommended Daily Dose:	0.264
Skin Sensitization:	0.352
Carcinogencity:	0.043
Eye Corrosion:	0.003
Eye Irritation:	0.073
Respiratory Toxicity:	0.294

Download Data

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

Natural Product: NPC311256

Natural Product ID:	NPC311256
*Common Name:**	(+)-Cycloolivil
IUPAC Name:	(2S,3S,4S)-4-(4-hydroxy-3-methoxyphenyl)-2,3-bis(hydroxymethyl)-7-methoxy-3,4-dihydro-1H-naphthalene-2,6-diol
Synonyms:	(+)-Cycloolivil
Standard InCHIKey:	KCIQZCNOUZCRGH-VOBQZIQPSA-N
Standard InCHI:	InChI=1S/C20H24O7/c1-26-17-5-11(3-4-15(17)23)19-13-7-16(24)18(27-2)6-12(13)8-20(25,10-22)14(19)9-21/h3-7,14,19,21-25H,8-10H2,1-2H3/t14-,19+,20-/m1/s1
SMILES:	COc1cc(ccc1O)[C@H]1c2cc(c(cc2C[C@@](CO)([C@@H]1CO)O)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL516536
PubChem CID:	5316262
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003425] Aryltetralin lignans [CHEMONTID:0003426] 9,9p-dihydroxyaryltetralin 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
NPO10969	Epimedium sagittatum	Species	Berberidaceae	Eukaryota	n.a.	leaf	n.a.	PMID[8699184]
NPO19434	Securinega suffruticosa	Species	Phyllanthaceae	Eukaryota	Twigs	n.a.	n.a.	PMID[31082231]
NPO12498	Carpesium cernuum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27668963]
NPO17434	Sambucus williamsii	Species	Adoxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26988298]
NPO16850	Eucommia ulmoides	Species	Eucommiaceae	Eukaryota	n.a.	bark	n.a.	PMID[26767291]
NPO16850	Eucommia ulmoides	Species	Eucommiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26767291]
NPO23024	Epimedium koreanum	Species	Berberidaceae	Eukaryota	aerial parts	herbal garden of Chungbuk National University, Cheongju, Korea	2012-Oct	PMID[24963714]
NPO1689	Epimedium pubescens	Species	Berberidaceae	Eukaryota	n.a.	leaf	n.a.	PMID[24066589]
NPO23024	Epimedium koreanum	Species	Berberidaceae	Eukaryota	n.a.	root	n.a.	PMID[22051934]
NPO1743	Neurospora terricola	Species	Sordariaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19795843]

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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	1
Others	1

Activity Type	# Activity
Individual Protein	1
NON-MOLECULAR	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	SC50	=	17.38	uM	PMID[558385]
NPT967	Individual Protein	Xanthine dehydrogenase	Homo sapiens	IC50	=	101380.0	nM	PMID[558385]

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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 NPC311256 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	408
0.1-0.2	1438
0.2-0.3	3637
0.3-0.4	9691
0.4-0.5	9076
0.5-0.6	4010
0.6-0.7	8631
0.7-0.8	4444
0.8-0.85	792
0.85-0.9	505
0.9-0.95	60
0.95-1	5

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Similarity Score	Similarity Level	Natural Product ID
0.9545	High Similarity	NPC184613
0.9528	High Similarity	NPC307050
0.9528	High Similarity	NPC277458
0.9449	High Similarity	NPC5428
0.9398	High Similarity	NPC230124

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 NPC311256 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	342
0.1-0.2	861
0.2-0.3	1685
0.3-0.4	2703
0.4-0.5	1764
0.5-0.6	943
0.6-0.7	678
0.7-0.8	164
0.8-0.85	9
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
0.8864	High Similarity	NPD3027	Phase 3
0.8667	High Similarity	NPD3619	Clinical (unspecified phase)
0.8667	High Similarity	NPD3620	Phase 2
0.8394	Intermediate Similarity	NPD1613	Approved
0.8394	Intermediate Similarity	NPD1612	Clinical (unspecified phase)

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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