NPASS Compound

Structure

CID232992 OpenBabel06191716032D 45 49 0 0 1 0 0 0 0 0999 V2000 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 5.0000 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 1.5000 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 -6.9282 2.0000 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 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 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 2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 3.5000 0.0000 C 0 0 1 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 3.4641 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 -6.9282 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 -6.0622 3.5000 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 2.5981 1.5000 0.0000 C 0 0 2 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 4.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 5.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 4.5000 0.0000 C 0 0 2 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 -0.0000 2.0000 0.0000 C 0 0 1 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 -0.8660 3.5000 0.0000 C 0 0 1 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 -1.7321 -1.0000 0.0000 O 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 -7.7942 3.5000 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 -2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 O 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 1.7321 2.0000 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 -1.7321 2.0000 0.0000 O 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 2 39 1 0 0 0 0 3 6 2 0 0 0 0 3 14 1 0 0 0 0 4 8 2 0 0 0 0 4 14 1 0 0 0 0 5 7 2 0 0 0 0 5 15 1 0 0 0 0 6 17 1 0 0 0 0 7 16 1 0 0 0 0 8 22 1 0 0 0 0 9 14 2 0 0 0 0 9 19 1 0 0 0 0 10 15 2 0 0 0 0 10 18 1 0 0 0 0 11 31 1 0 0 0 0 12 21 1 0 0 0 0 12 40 1 0 0 0 0 13 1 1 1 0 0 0 13 23 1 0 0 0 0 13 41 1 0 0 0 0 16 18 2 0 0 0 0 16 32 1 0 0 0 0 17 19 2 0 0 0 0 17 33 1 0 0 0 0 18 34 1 0 0 0 0 19 39 1 0 0 0 0 20 11 1 6 0 0 0 20 26 1 0 0 0 0 20 43 1 0 0 0 0 21 15 1 1 0 0 0 21 42 1 0 0 0 0 22 35 2 0 0 0 0 22 44 1 0 0 0 0 23 24 1 0 0 0 0 23 36 1 6 0 0 0 24 25 1 0 0 0 0 24 37 1 1 0 0 0 25 29 1 0 0 0 0 25 38 1 1 0 0 0 26 27 1 0 0 0 0 26 44 1 1 0 0 0 27 28 1 0 0 0 0 27 45 1 6 0 0 0 28 30 1 0 0 0 0 28 42 1 1 0 0 0 29 41 1 0 0 0 0 29 45 1 6 0 0 0 30 40 1 6 0 0 0 30 43 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	636.21
Volume:	595.415
LogP:	1.238
LogD:	0.271
LogS:	-2.828
# Rotatable Bonds:	9
TPSA:	223.29
# H-Bond Aceptor:	15
# H-Bond Donor:	7
# Rings:	5
# Heavy Atoms:	15

MedChem Properties

QED Drug-Likeness Score:	0.113
Synthetic Accessibility Score:	4.974
Fsp3:	0.5
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	2
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.537
MDCK Permeability:	4.2585099436109886e-05
Pgp-inhibitor:	0.014
Pgp-substrate:	0.999
Human Intestinal Absorption (HIA):	0.888
20% Bioavailability (F20%):	0.022
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.091
Plasma Protein Binding (PPB):	93.7818374633789%
Volume Distribution (VD):	0.361
Pgp-substrate:	10.199773788452148%

ADMET: Metabolism

CYP1A2-inhibitor:	0.034
CYP1A2-substrate:	0.052
CYP2C19-inhibitor:	0.068
CYP2C19-substrate:	0.062
CYP2C9-inhibitor:	0.159
CYP2C9-substrate:	0.103
CYP2D6-inhibitor:	0.034
CYP2D6-substrate:	0.19
CYP3A4-inhibitor:	0.142
CYP3A4-substrate:	0.067

ADMET: Excretion

Clearance (CL):	1.96
Half-life (T1/2):	0.818

ADMET: Toxicity

hERG Blockers:	0.243
Human Hepatotoxicity (H-HT):	0.276
Drug-inuced Liver Injury (DILI):	0.855
AMES Toxicity:	0.618
Rat Oral Acute Toxicity:	0.069
Maximum Recommended Daily Dose:	0.044
Skin Sensitization:	0.962
Carcinogencity:	0.09
Eye Corrosion:	0.003
Eye Irritation:	0.029
Respiratory Toxicity:	0.191

Download Data

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

Natural Product: NPC232992

Natural Product ID:	NPC232992
*Common Name:**	1,2-O-[2S-(3,4-Dihydroxyphenyl)-1,2-Ethanediyl]-3-O-Alpha-L-Rhamnopyranosyl-4-O-Feruloyl-Alpha-D-Glucopyranoside
IUPAC Name:	[(2S,4aR,6R,7R,8S,8aR)-2-(3,4-dihydroxyphenyl)-6-(hydroxymethyl)-8-[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy-3,4a,6,7,8,8a-hexahydro-2H-pyrano[2,3-b][1,4]dioxin-7-yl] (E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoate
Synonyms:	3''-O-methylcrenatoside
Standard InCHIKey:	UJSFZPXZSSCWGS-BRLAKEAASA-N
Standard InCHI:	InChI=1S/C30H36O15/c1-13-23(36)24(37)25(38)29(41-13)45-27-26(44-22(35)8-4-14-3-6-17(33)19(9-14)39-2)20(11-31)43-30-28(27)42-21(12-40-30)15-5-7-16(32)18(34)10-15/h3-10,13,20-21,23-34,36-38H,11-12H2,1-2H3/b8-4+/t13-,20+,21+,23-,24+,25+,26+,27-,28+,29-,30+/m0/s1
SMILES:	OC[C@H]1O[C@H]2OC[C@@H](O[C@@H]2[C@H]([C@@H]1OC(=O)/C=C/c1ccc(c(c1)OC)O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)O)c1ccc(c(c1)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL502701
PubChem CID:	10326741
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000476] Cinnamic acids and derivatives [CHEMONTID:0001391] Hydroxycinnamic acids and derivatives [CHEMONTID:0000059] Coumaric acids and derivatives

*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
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30188125]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[15577255]
NPO21245	Microtoena prainiana	Species	Lamiaceae	Eukaryota	stems	n.a.	n.a.	PMID[15217277]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[12575075]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	stem	n.a.	PMID[12575075]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21245	Microtoena prainiana	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]

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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
Others	3

Activity Type	# Activity
Individual Protein	3

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1166	Individual Protein	Angiotensin-converting enzyme	Homo sapiens	Inhibition	=	99.8	%	PMID[465001]
NPT1166	Individual Protein	Angiotensin-converting enzyme	Homo sapiens	Inhibition	=	67.5	%	PMID[465001]
NPT1166	Individual Protein	Angiotensin-converting enzyme	Homo sapiens	Inhibition	=	32.5	%	PMID[465001]

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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 NPC232992 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	342
0.1-0.2	1476
0.2-0.3	3538
0.3-0.4	8221
0.4-0.5	9087
0.5-0.6	7040
0.6-0.7	8229
0.7-0.8	4059
0.8-0.85	504
0.85-0.9	116
0.9-0.95	51
0.95-1	34

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Similarity Score	Similarity Level	Natural Product ID
0.9858	High Similarity	NPC476386
0.9858	High Similarity	NPC473427
0.9858	High Similarity	NPC259347
0.9858	High Similarity	NPC476398
0.9858	High Similarity	NPC94871

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 NPC232992 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	283
0.1-0.2	851
0.2-0.3	1759
0.3-0.4	2849
0.4-0.5	1869
0.5-0.6	1042
0.6-0.7	438
0.7-0.8	56
0.8-0.85	2
0.85-0.9	0
0.9-0.95	1
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9424	High Similarity	NPD7266	Discontinued
0.8543	High Similarity	NPD1653	Approved
0.8395	Intermediate Similarity	NPD7074	Phase 3
0.8333	Intermediate Similarity	NPD7054	Approved
0.8282	Intermediate Similarity	NPD7472	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