NPASS Compound

Structure

CID111112 OpenBabel06191715462D 40 45 0 0 0 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 -2.5000 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 -4.3301 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 1.7321 -1.0000 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 6.0622 -1.5000 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 2.0000 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 -3.4641 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 -5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -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 0.8660 -2.5000 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 -0.8660 -1.5000 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 -0.8660 1.5000 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 3.4641 -1.0000 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 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 0 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 0.0000 0.0000 0.0000 C 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 -1.5000 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 6.0622 1.5000 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 4.3301 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 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 -2.5981 0.5000 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 1 4 1 0 0 0 0 1 13 2 0 0 0 0 2 5 2 0 0 0 0 2 13 1 0 0 0 0 3 6 2 0 0 0 0 3 14 1 0 0 0 0 4 15 2 0 0 0 0 5 15 1 0 0 0 0 6 18 1 0 0 0 0 7 14 2 0 0 0 0 7 17 1 0 0 0 0 8 16 2 0 0 0 0 8 19 1 0 0 0 0 9 16 1 0 0 0 0 9 25 2 0 0 0 0 10 21 1 0 0 0 0 10 24 2 0 0 0 0 11 22 1 0 0 0 0 11 23 2 0 0 0 0 12 20 2 0 0 0 0 12 26 1 0 0 0 0 13 23 1 0 0 0 0 14 24 1 0 0 0 0 15 31 1 0 0 0 0 16 32 1 0 0 0 0 17 18 2 0 0 0 0 17 27 1 0 0 0 0 18 33 1 0 0 0 0 19 28 2 0 0 0 0 19 34 1 0 0 0 0 20 27 1 0 0 0 0 20 35 1 0 0 0 0 21 28 1 0 0 0 0 21 36 2 0 0 0 0 22 29 1 0 0 0 0 22 37 2 0 0 0 0 23 39 1 0 0 0 0 24 40 1 0 0 0 0 25 28 1 0 0 0 0 25 40 1 0 0 0 0 26 29 2 0 0 0 0 26 39 1 0 0 0 0 27 30 2 0 0 0 0 29 30 1 0 0 0 0 30 38 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	538.09
Volume:	521.816
LogP:	6.077
LogD:	2.301
LogS:	-4.004
# Rotatable Bonds:	3
TPSA:	181.8
# H-Bond Aceptor:	10
# H-Bond Donor:	6
# Rings:	6
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.177
Synthetic Accessibility Score:	3.034
Fsp3:	0.0
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.259
MDCK Permeability:	8.156965122907422e-06
Pgp-inhibitor:	0.021
Pgp-substrate:	0.02
Human Intestinal Absorption (HIA):	0.565
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001
Plasma Protein Binding (PPB):	98.79447937011719%
Volume Distribution (VD):	0.463
Pgp-substrate:	4.027957439422607%

ADMET: Metabolism

CYP1A2-inhibitor:	0.895
CYP1A2-substrate:	0.101
CYP2C19-inhibitor:	0.642
CYP2C19-substrate:	0.034
CYP2C9-inhibitor:	0.554
CYP2C9-substrate:	0.879
CYP2D6-inhibitor:	0.161
CYP2D6-substrate:	0.462
CYP3A4-inhibitor:	0.236
CYP3A4-substrate:	0.057

ADMET: Excretion

Clearance (CL):	2.862
Half-life (T1/2):	0.521

ADMET: Toxicity

hERG Blockers:	0.164
Human Hepatotoxicity (H-HT):	0.078
Drug-inuced Liver Injury (DILI):	0.984
AMES Toxicity:	0.191
Rat Oral Acute Toxicity:	0.031
Maximum Recommended Daily Dose:	0.83
Skin Sensitization:	0.922
Carcinogencity:	0.037
Eye Corrosion:	0.003
Eye Irritation:	0.908
Respiratory Toxicity:	0.035

Download Data

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

Natural Product: NPC111112

Natural Product ID:	NPC111112
*Common Name:**	Robustaflavone
IUPAC Name:	6-[5-(5,7-dihydroxy-4-oxochromen-2-yl)-2-hydroxyphenyl]-5,7-dihydroxy-2-(4-hydroxyphenyl)chromen-4-one
Synonyms:	Robustaflavone
Standard InCHIKey:	BORWSEZUWHQTOK-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C30H18O10/c31-15-4-1-13(2-5-15)23-11-22(37)29-26(39-23)12-20(35)27(30(29)38)17-7-14(3-6-18(17)33)24-10-21(36)28-19(34)8-16(32)9-25(28)40-24/h1-12,31-35,38H
SMILES:	Oc1ccc(cc1)c1cc(=O)c2c(o1)cc(c(c2O)c1cc(ccc1O)c1cc(=O)c2c(o1)cc(cc2O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL63677
PubChem CID:	5281694
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001586] Biflavonoids and polyflavonoids

*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
NPO33250	rhus succedanea	Species	Anacardiaceae	Eukaryota	seed kernels	Fukuoka, Japan	n.a.	PMID[9322359]
NPO9740	Dacrycarpus imbricatus	Species	Podocarpaceae	Eukaryota	Twigs	n.a.	n.a.	PMID[32786878]
NPO14158	Selaginella tamariscina	Species	Selaginellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31244143]
NPO40105	Dietes bicolor	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29381070]
NPO28400	Selaginella pulvinata	Species	Selaginellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29144743]
NPO7175	Eucalyptus robusta	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27142786]
NPO14158	Selaginella tamariscina	Species	Selaginellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25559759]
NPO29798	Podocarpus imbricatus	Species	Podocarpaceae	Eukaryota	twigs and leaves	n.a.	n.a.	PMID[24953598]
NPO28400	Selaginella pulvinata	Species	Selaginellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20335035]
NPO33250	rhus succedanea	Species	Anacardiaceae	Eukaryota	sap	n.a.	n.a.	PMID[12444713]

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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
EC50	2
IC50	23
Ki	1
Others	44

Activity Type	# Activity
Cell Line	36
Individual Protein	23
Organism	6
Others	5

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT3140	Cell Line	MGC-803	Homo sapiens	IC50	=	15570.0	nM	PMID[489828]
NPT65	Cell Line	HepG2	Homo sapiens	IC50	=	19150.0	nM	PMID[489828]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	21380.0	nM	PMID[489828]
NPT550	Cell Line	T-24	Homo sapiens	IC50	=	21090.0	nM	PMID[489828]
NPT568	Individual Protein	Matrix metalloproteinase-2	Homo sapiens	IC50	=	10220.0	nM	PMID[489828]
NPT280	Individual Protein	Matrix metalloproteinase 9	Homo sapiens	IC50	=	11850.0	nM	PMID[489828]
NPT521	Cell Line	RBL-2H3	Rattus norvegicus	Inhibition	=	5.3	%	PMID[489827]
NPT521	Cell Line	RBL-2H3	Rattus norvegicus	Inhibition	=	6.0	%	PMID[489827]
NPT521	Cell Line	RBL-2H3	Rattus norvegicus	Inhibition	=	2.7	%	PMID[489827]
NPT521	Cell Line	RBL-2H3	Rattus norvegicus	Inhibition	=	45.3	%	PMID[489827]

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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 NPC111112 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	569
0.1-0.2	2160
0.2-0.3	4953
0.3-0.4	11866
0.4-0.5	5773
0.5-0.6	4527
0.6-0.7	5612
0.7-0.8	4240
0.8-0.85	2153
0.85-0.9	716
0.9-0.95	95
0.95-1	33

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC222713
1.0	High Similarity	NPC138299
1.0	High Similarity	NPC67322
0.9863	High Similarity	NPC194593
0.9863	High Similarity	NPC290830

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 NPC111112 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	514
0.1-0.2	1004
0.2-0.3	1692
0.3-0.4	2756
0.4-0.5	1836
0.5-0.6	935
0.6-0.7	262
0.7-0.8	103
0.8-0.85	34
0.85-0.9	13
0.9-0.95	1
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9184	High Similarity	NPD7410	Clinical (unspecified phase)
0.9054	High Similarity	NPD4378	Clinical (unspecified phase)
0.8974	High Similarity	NPD6959	Discontinued
0.8924	High Similarity	NPD7852	Clinical (unspecified phase)
0.8896	High Similarity	NPD8443	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