NPASS Compound

Structure

NPC18699 OpenBabel07101719152D 43 48 0 0 0 0 0 0 0 0999 V2000 -5.0901 0.9796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8484 2.4490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0901 -3.9184 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6967 0.9796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5451 -0.4898 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5451 1.4694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3934 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6967 2.9388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5451 2.4490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8484 1.4694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7868 -1.9592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0901 -1.9592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5451 -1.4694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8484 -1.4694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0901 0.9796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6967 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3934 0.9796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8484 2.4490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9385 -2.4490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5451 1.4694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6967 0.9796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7868 -0.9796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5451 -0.4898 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6967 -1.9592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9385 0.4898 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.9592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8484 -0.4898 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2418 0.4898 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0901 -0.9796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6967 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9385 -0.4898 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8484 -1.4694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8484 -0.4898 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6352 -0.4898 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3934 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6967 -2.9388 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.7868 0.9796 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.9388 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2418 1.4694 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.9388 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9385 -3.4286 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2418 -0.4898 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 6 1 0 0 0 0 4 16 2 0 0 0 0 5 7 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 9 2 0 0 0 0 8 18 1 0 0 0 0 9 20 1 0 0 0 0 10 18 2 0 0 0 0 10 21 1 0 0 0 0 11 19 2 0 0 0 0 11 22 1 0 0 0 0 12 19 1 0 0 0 0 12 29 2 0 0 0 0 13 23 2 0 0 0 0 13 24 1 0 0 0 0 14 26 1 0 0 0 0 14 27 2 0 0 0 0 15 25 1 0 0 0 0 15 28 2 0 0 0 0 16 27 1 0 0 0 0 17 39 1 0 0 0 0 18 40 1 0 0 0 0 19 41 1 0 0 0 0 20 21 2 0 0 0 0 20 28 1 0 0 0 0 21 30 1 0 0 0 0 22 31 2 0 0 0 0 22 34 1 0 0 0 0 23 30 1 0 0 0 0 23 35 1 0 0 0 0 24 32 2 0 0 0 0 24 36 1 0 0 0 0 25 31 1 0 0 0 0 25 37 2 0 0 0 0 26 32 1 0 0 0 0 26 38 2 0 0 0 0 27 43 1 0 0 0 0 28 42 1 0 0 0 0 29 31 1 0 0 0 0 29 42 1 0 0 0 0 30 33 2 0 0 0 0 32 33 1 0 0 0 0 33 43 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	580.14
Volume:	573.704
LogP:	6.637
LogD:	2.725
LogS:	-5.716
# Rotatable Bonds:	6
TPSA:	148.8
# H-Bond Aceptor:	10
# H-Bond Donor:	3
# Rings:	6
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.213
Synthetic Accessibility Score:	2.971
Fsp3:	0.091
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:	-4.98
MDCK Permeability:	2.8769347409252077e-05
Pgp-inhibitor:	0.978
Pgp-substrate:	0.066
Human Intestinal Absorption (HIA):	0.106
20% Bioavailability (F20%):	0.026
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0
Plasma Protein Binding (PPB):	91.53190612792969%
Volume Distribution (VD):	0.389
Pgp-substrate:	9.507492065429688%

ADMET: Metabolism

CYP1A2-inhibitor:	0.75
CYP1A2-substrate:	0.872
CYP2C19-inhibitor:	0.737
CYP2C19-substrate:	0.051
CYP2C9-inhibitor:	0.696
CYP2C9-substrate:	0.956
CYP2D6-inhibitor:	0.054
CYP2D6-substrate:	0.947
CYP3A4-inhibitor:	0.24
CYP3A4-substrate:	0.14

ADMET: Excretion

Clearance (CL):	3.803
Half-life (T1/2):	0.083

ADMET: Toxicity

hERG Blockers:	0.055
Human Hepatotoxicity (H-HT):	0.423
Drug-inuced Liver Injury (DILI):	0.986
AMES Toxicity:	0.292
Rat Oral Acute Toxicity:	0.029
Maximum Recommended Daily Dose:	0.912
Skin Sensitization:	0.31
Carcinogencity:	0.03
Eye Corrosion:	0.003
Eye Irritation:	0.613
Respiratory Toxicity:	0.124

Download Data

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

Natural Product: NPC18699

Natural Product ID:	NPC18699
*Common Name:**	5,7-Dihydroxy-8-[2-(5-Hydroxy-7-Methoxy-4-Oxochromen-2-Yl)-5-Methoxyphenyl]-2-(4-Methoxyphenyl)Chromen-4-One
IUPAC Name:	5,7-dihydroxy-8-[2-(5-hydroxy-7-methoxy-4-oxochromen-2-yl)-5-methoxyphenyl]-2-(4-methoxyphenyl)chromen-4-one
Synonyms:
Standard InCHIKey:	LDDWBTHCKGZOCL-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C33H24O10/c1-39-17-6-4-16(5-7-17)27-14-26(38)32-24(36)13-23(35)30(33(32)43-27)21-10-18(40-2)8-9-20(21)28-15-25(37)31-22(34)11-19(41-3)12-29(31)42-28/h4-15,34-36H,1-3H3
SMILES:	COc1ccc(c(c1)c1c(O)cc(c2c1oc(cc2=O)c1ccc(cc1)OC)O)c1cc(=O)c2c(o1)cc(cc2O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL316312
PubChem CID:	44327242
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0002585] O-methylated flavonoids [CHEMONTID:0002592] 7-O-methylated flavonoids

*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
NPO29841	Taxus yunnanensis	Species	Taxaceae	Eukaryota	wood	Yunnang Province, China	2000-OCT	PMID[21138310]
NPO29841	Taxus yunnanensis	Species	Taxaceae	Eukaryota	n.a.	xylem	n.a.	PMID[21138310]
NPO29841	Taxus yunnanensis	Species	Taxaceae	Eukaryota	wood	n.a.	n.a.	PMID[12444707]
NPO29841	Taxus yunnanensis	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12217376]
NPO31343	Taxus chinensis	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12217376]
NPO29841	Taxus yunnanensis	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO31343	Taxus chinensis	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29841	Taxus yunnanensis	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO31343	Taxus chinensis	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]

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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
ED50	8
Others	8

Activity Type	# Activity
Cell Line	12
NON-MOLECULAR	2
Others	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1178	Cell Line	KB 3-1	Homo sapiens	ED50	>	20.0	ug ml-1	PMID[485416]
NPT1178	Cell Line	KB 3-1	Homo sapiens	Inhibition	=	9.0	%	PMID[485416]
NPT81	Cell Line	A549	Homo sapiens	ED50	>	20.0	ug ml-1	PMID[485416]
NPT81	Cell Line	A549	Homo sapiens	Inhibition	=	58.0	%	PMID[485416]
NPT83	Cell Line	MCF7	Homo sapiens	ED50	>	20.0	ug ml-1	PMID[485416]
NPT83	Cell Line	MCF7	Homo sapiens	Inhibition	=	22.0	%	PMID[485416]
NPT147	Cell Line	SK-MEL-2	Homo sapiens	ED50	>	20.0	ug ml-1	PMID[485416]
NPT147	Cell Line	SK-MEL-2	Homo sapiens	Inhibition	=	9.0	%	PMID[485416]
NPT307	Cell Line	HOS	Homo sapiens	ED50	>	20.0	ug ml-1	PMID[485416]
NPT307	Cell Line	HOS	Homo sapiens	Inhibition	=	25.0	%	PMID[485416]

Showing 1 to 10 of 16 entries

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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 NPC18699 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	492
0.1-0.2	2024
0.2-0.3	4511
0.3-0.4	10984
0.4-0.5	6999
0.5-0.6	4227
0.6-0.7	5515
0.7-0.8	4606
0.8-0.85	2539
0.85-0.9	722
0.9-0.95	72
0.95-1	6

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC55443
0.98	High Similarity	NPC254351
0.9739	High Similarity	NPC273467
0.9739	High Similarity	NPC189552
0.9673	High Similarity	NPC186325

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 NPC18699 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	464
0.1-0.2	1011
0.2-0.3	1652
0.3-0.4	2714
0.4-0.5	1865
0.5-0.6	975
0.6-0.7	292
0.7-0.8	126
0.8-0.85	41
0.85-0.9	9
0.9-0.95	1
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9236	High Similarity	NPD6959	Discontinued
0.8947	High Similarity	NPD7410	Clinical (unspecified phase)
0.8944	High Similarity	NPD7852	Clinical (unspecified phase)
0.8917	High Similarity	NPD8443	Clinical (unspecified phase)
0.8854	High Similarity	NPD7819	Suspended

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