NPASS Compound

Structure

CID270675 OpenBabel06191716072D 42 46 0 0 1 0 0 0 0 0999 V2000 -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 -2.5981 1.5000 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 6.9282 2.0000 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 -4.3301 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 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 3.0000 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 5.1962 3.0000 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 -3.4641 2.0000 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 -5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 0.5000 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 3.5000 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 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 0.0000 -1.0000 0.0000 C 0 0 2 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 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 2 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 1.7321 0.0000 0.0000 C 0 0 2 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 -6.0622 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 4.5000 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 0.8660 -2.5000 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 2.5981 0.5000 0.0000 O 0 0 0 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 0.8660 1.5000 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 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 1 0 0 0 0 1 15 2 0 0 0 0 2 7 2 0 0 0 0 2 15 1 0 0 0 0 3 10 2 0 0 0 0 3 15 1 0 0 0 0 4 8 1 0 0 0 0 4 16 2 0 0 0 0 5 9 2 0 0 0 0 5 16 1 0 0 0 0 6 17 2 0 0 0 0 7 17 1 0 0 0 0 8 18 2 0 0 0 0 9 18 1 0 0 0 0 10 25 1 0 0 0 0 11 19 2 0 0 0 0 11 20 1 0 0 0 0 12 19 1 0 0 0 0 12 23 2 0 0 0 0 13 21 1 0 0 0 0 13 22 2 0 0 0 0 14 39 1 0 0 0 0 16 22 1 0 0 0 0 17 31 1 0 0 0 0 18 32 1 0 0 0 0 19 40 1 0 0 0 0 20 26 2 0 0 0 0 20 33 1 0 0 0 0 21 26 1 0 0 0 0 21 34 2 0 0 0 0 22 41 1 0 0 0 0 23 26 1 0 0 0 0 23 41 1 0 0 0 0 24 14 1 1 0 0 0 24 27 1 0 0 0 0 24 42 1 0 0 0 0 25 35 2 0 0 0 0 25 39 1 0 0 0 0 27 28 1 0 0 0 0 27 36 1 6 0 0 0 28 29 1 0 0 0 0 28 37 1 1 0 0 0 29 30 1 0 0 0 0 29 38 1 6 0 0 0 30 40 1 1 0 0 0 30 42 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	578.14
Volume:	555.862
LogP:	3.603
LogD:	2.561
LogS:	-4.418
# Rotatable Bonds:	8
TPSA:	196.35
# H-Bond Aceptor:	12
# H-Bond Donor:	6
# Rings:	5
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.138
Synthetic Accessibility Score:	4.081
Fsp3:	0.2
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:	-6.134
MDCK Permeability:	1.7775337255443446e-05
Pgp-inhibitor:	0.004
Pgp-substrate:	0.915
Human Intestinal Absorption (HIA):	0.391
20% Bioavailability (F20%):	0.848
30% Bioavailability (F30%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.012
Plasma Protein Binding (PPB):	100.83959197998047%
Volume Distribution (VD):	0.626
Pgp-substrate:	1.8221650123596191%

ADMET: Metabolism

CYP1A2-inhibitor:	0.681
CYP1A2-substrate:	0.036
CYP2C19-inhibitor:	0.453
CYP2C19-substrate:	0.052
CYP2C9-inhibitor:	0.644
CYP2C9-substrate:	0.914
CYP2D6-inhibitor:	0.803
CYP2D6-substrate:	0.449
CYP3A4-inhibitor:	0.559
CYP3A4-substrate:	0.089

ADMET: Excretion

Clearance (CL):	4.379
Half-life (T1/2):	0.667

ADMET: Toxicity

hERG Blockers:	0.217
Human Hepatotoxicity (H-HT):	0.145
Drug-inuced Liver Injury (DILI):	0.834
AMES Toxicity:	0.684
Rat Oral Acute Toxicity:	0.039
Maximum Recommended Daily Dose:	0.065
Skin Sensitization:	0.956
Carcinogencity:	0.516
Eye Corrosion:	0.003
Eye Irritation:	0.308
Respiratory Toxicity:	0.029

Download Data

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

Natural Product: NPC270675

Natural Product ID:	NPC270675
*Common Name:**	Cosmosiin 6''-(E)-P-Coumarate
IUPAC Name:	[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-[5-hydroxy-2-(4-hydroxyphenyl)-4-oxochromen-7-yl]oxyoxan-2-yl]methyl (E)-3-(4-hydroxyphenyl)prop-2-enoate
Synonyms:
Standard InCHIKey:	WPQRDUGBKUNFJW-ZZSHFKPLSA-N
Standard InCHI:	InChI=1S/C30H26O12/c31-17-6-1-15(2-7-17)3-10-25(35)39-14-24-27(36)28(37)29(38)30(42-24)40-19-11-20(33)26-21(34)13-22(41-23(26)12-19)16-4-8-18(32)9-5-16/h1-13,24,27-33,36-38H,14H2/b10-3+/t24-,27-,28+,29-,30-/m1/s1
SMILES:	O=C(OC[C@H]1O[C@@H](Oc2cc(O)c3c(c2)oc(cc3=O)c2ccc(cc2)O)[C@@H]([C@H]([C@@H]1O)O)O)/C=C/c1ccc(cc1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3597472
PubChem CID:	6439941
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003533] Flavonoid-7-O-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
NPO2804	Calophyllum inophyllum	Species	Calophyllaceae	Eukaryota	n.a.	Malaysian	n.a.	PMID[7506311]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30188125]
NPO26700	Tinospora crispa	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29397715]
NPO26700	Tinospora crispa	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28742368]
NPO26700	Tinospora crispa	Species	Menispermaceae	Eukaryota	leaf	Putz City, Chiayi County, Taiwan	2009-Nov	PMID[25999202]
NPO19792	Populus tomentosa	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22860454]
NPO3123	Anthemis cretica	Species	Asteraceae	Eukaryota	n.a.	aerial part	n.a.	PMID[22351977]
NPO26700	Tinospora crispa	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22283497]
NPO26700	Tinospora crispa	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20356064]
NPO2804	Calophyllum inophyllum	Species	Calophyllaceae	Eukaryota	n.a.	stem	n.a.	PMID[20188156]

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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	1

Activity Type	# Activity
Others	3

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified	""	IC50	=	14600.0	nM	PMID[468274]
NPT27	Others	Unspecified	""	IC50	=	42000.0	nM	PMID[468274]
NPT35	Others	n.a.	""	Retention_time	=	43.4	min	PMID[468274]

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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 NPC270675 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	395
0.1-0.2	1617
0.2-0.3	3881
0.3-0.4	8714
0.4-0.5	9691
0.5-0.6	4629
0.6-0.7	5749
0.7-0.8	5296
0.8-0.85	1705
0.85-0.9	696
0.9-0.95	270
0.95-1	54

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC477628
1.0	High Similarity	NPC195685
1.0	High Similarity	NPC210961
1.0	High Similarity	NPC472994
1.0	High Similarity	NPC477629

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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 NPC270675 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	356
0.1-0.2	905
0.2-0.3	1795
0.3-0.4	2677
0.4-0.5	1957
0.5-0.6	994
0.6-0.7	286
0.7-0.8	130
0.8-0.85	33
0.85-0.9	16
0.9-0.95	1
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9545	High Similarity	NPD4381	Clinical (unspecified phase)
0.9018	High Similarity	NPD7804	Clinical (unspecified phase)
0.9018	High Similarity	NPD7054	Approved
0.8963	High Similarity	NPD7472	Approved
0.8916	High Similarity	NPD4338	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