NPASS Compound

Natural Product: NPC572083

Natural Product ID	NPC572083
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	3,5,7-trihydroxy-2-(4-methoxyphenyl)-8-[[3,5,7-trihydroxy-2-(4-methoxyphenyl)-4-oxo-chromen-8-yl]methyl]chromen-4-one
IUPAC Name	3,5,7-trihydroxy-2-(4-methoxyphenyl)-8-[[3,5,7-trihydroxy-2-(4-methoxyphenyl)-4-oxo-chromen-8-yl]methyl]chromen-4-one
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 69 74 0 0 0 0 0 0 0 0999 V2000 6.6541 -1.8493 4.0965 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0693 -0.7670 3.2975 O 0 0 0 0 0 0 0 0 0 0 0 0 6.2427 -0.1278 2.3877 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7148 0.9064 1.6543 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8667 1.5394 0.7413 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5807 1.1708 0.5463 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6404 1.7654 -0.3695 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9410 2.8203 -1.1876 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1939 3.4315 -1.2199 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9959 3.3744 -2.0690 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2713 4.3320 -2.8107 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7381 2.8236 -2.0926 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7352 3.2925 -2.9162 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0470 4.3717 -3.7509 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5054 2.7146 -2.9038 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7276 1.6490 -2.0455 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9819 1.0983 -2.0630 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2218 1.1324 -1.2016 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0213 0.0373 -0.2704 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1413 -1.3070 -0.8122 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8873 -2.0203 -1.3678 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1761 -1.5181 -1.4831 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7424 -3.3158 -1.8702 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4978 -3.8947 -1.7987 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7014 -5.1802 -2.2826 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5537 -3.1695 -1.2307 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4198 -1.8970 -0.7348 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4128 -1.2391 -0.2078 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6115 -1.7861 -0.1306 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6542 -0.9674 0.4760 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3332 0.3250 0.9328 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2458 1.1543 1.5105 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5584 0.7800 1.6886 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4762 1.6274 2.2752 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.1715 2.9162 2.7347 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9090 -0.4719 1.2562 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9590 -1.3239 0.6596 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8351 -3.0497 -0.6002 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0587 -3.6789 -0.5509 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7744 -3.7696 -1.1701 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9269 -4.9316 -1.6154 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4776 1.7610 -1.2514 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3949 1.2934 -0.4584 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1276 0.0964 1.3234 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9444 -0.5416 2.2281 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9921 -1.4993 4.9137 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0776 -2.6169 3.5166 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5254 -2.3316 4.5911 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7530 1.2518 1.7690 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3029 2.3517 0.1917 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8256 3.2746 -2.0040 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3048 4.2293 -4.7142 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2813 3.0839 -3.5462 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2588 0.6189 -2.9306 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8461 -0.0251 0.5062 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8732 0.3119 0.3657 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0035 -1.9607 -1.1655 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5645 -3.8665 -2.3061 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6157 -5.9365 -1.6058 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3106 0.6581 0.8113 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9922 2.1624 1.8659 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7176 3.5260 1.9212 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0769 3.4045 3.1471 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4496 2.8203 3.5729 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9107 -0.8545 1.3517 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2951 -2.2943 0.3408 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3743 -4.2660 -1.3225 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1147 -0.2775 1.2447 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6169 -1.3715 2.8381 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 8 10 1 0 10 11 2 0 10 12 1 0 12 13 2 0 13 14 1 0 13 15 1 0 15 16 2 0 16 17 1 0 16 18 1 0 18 19 1 0 19 20 1 0 20 21 2 0 21 22 1 0 21 23 1 0 23 24 2 0 24 25 1 0 24 26 1 0 26 27 2 0 27 28 1 0 28 29 1 0 29 30 1 0 30 31 2 0 31 32 1 0 32 33 2 0 33 34 1 0 34 35 1 0 33 36 1 0 36 37 2 0 29 38 2 0 38 39 1 0 38 40 1 0 40 41 2 0 18 42 2 0 42 43 1 0 6 44 1 0 44 45 2 0 45 3 1 0 43 7 1 0 42 12 1 0 27 20 1 0 37 30 1 0 40 26 1 0 1 46 1 0 1 47 1 0 1 48 1 0 4 49 1 0 5 50 1 0 9 51 1 0 14 52 1 0 15 53 1 0 17 54 1 0 19 55 1 0 19 56 1 0 22 57 1 0 23 58 1 0 25 59 1 0 31 60 1 0 32 61 1 0 35 62 1 0 35 63 1 0 35 64 1 0 36 65 1 0 37 66 1 0 39 67 1 0 44 68 1 0 45 69 1 0 M END

Standard InCHIKey	UNTGWZYMPURTGA-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C33H24O12/c1-42-16-7-3-14(4-8-16)30-28(40)26(38)24-22(36)12-20(34)18(32(24)44-30)11-19-21(35)13-23(37)25-27(39)29(41)31(45-33(19)25)15-5-9-17(43-2)10-6-15/h3-10,12-13,34-37,40-41H,11H2,1-2H3
SMILES	COC1=CC=C(C2=C(O)C(=O)C3=C(O)C=C(O)C(CC4=C(O)C=C(O)C5=C4OC(C4=CC=C(OC)C=C4)=C(O)C5=O)=C3O2)C=C1

Calculated Properties

Physi-Chem Properties

Molecular Weight:	612.13	Volume:	591.285 ? Van der Waals volume.
Dense:	1.035	LogP:	3.435 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.46 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.495 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	36.0
TPSA:	200.26 ? Topological Polar Surface Area.	H-Bond Acceptor:	12.0
H-Bond Donor:	6.0	Rings:	6.0
Heavy Atoms:	12.0

MedChem Properties

QED Drug-Likeness Score:	0.146	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.154	Fsp³:	0.091
MCE-18:	38.0 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	1
Chelating Alert:	1	PAINS Alert:	0
Colloidal aggregators:	0.993	Fluc inhibitor:	0.803 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.99 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.995 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.23	Promiscuous compounds:	0.32

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.68	MDCK Permeability:	-4.961
Pgp-inhibitor:	0.995	Pgp-substrate:	0.01
PAMPA:	0.227 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.273
20% Bioavailability (F20%):	0.042	30% Bioavailability (F30%):	0.938
50% Bioavailability (F50%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.983
Plasma Protein Binding (PPB):	98.202%	Volume Distribution (VD):	-0.595
Fu:	0.804% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.999
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.997
BSEP inhibitor:	0.998

ADMET: Metabolism

CYP1A2-inhibitor:	0.688	CYP1A2-substrate:	0.148
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	1.0
CYP2C9-inhibitor:	0.999	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.993	CYP2D6-substrate:	0.492
CYP3A4-inhibitor:	0.004	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.999 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

0.917

Half-life (T1/2):

2.391

ADMET: Toxicity

hERG Blockers:	0.04	hERG Blockers (10um):	0.491
Human Hepatotoxicity (H-HT):	0.407	Drug-induced Liver Injury (DILI):	0.926
AMES Toxicity:	0.642	Rat Oral Acute Toxicity:	0.428
Maximum Recommended Daily Dose:	0.619	Skin Sensitization:	0.233
Carcinogencity:	0.421	Eye Corrosion:	0.0
Eye Irritation:	0.752	Respiratory Toxicity:	0.997
Drug-induced Neurotoxicity:	0.002	Ototoxicity:	0.055
Hematotoxicity:	0.049	Drug-induced Nephrotoxicity:	0.024
Genotoxicity:	0.995	RPMI-8226 Immunitoxicity:	0.12
A549 Cytotoxicity:	0.288	Hek293 Cytotoxicity:	0.791
BCF:	1.094 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	4.902 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.657 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.449 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO21049	Pentagramma triangularis	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO21049	Pentagramma triangularis	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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

Organism ID	Organism Name	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

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

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC572083 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	24511
0.1-0.2	21361
0.2-0.3	3288
0.3-0.4	576
0.4-0.5	100
0.5-0.6	15
0.6-0.7	3
0.7-0.8	1
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.7288	Intermediate Similarity	NPC607815
0.7049	Intermediate Similarity	NPC273538
0.6552	Remote Similarity	NPC201451
0.6552	Remote Similarity	NPC241838
0.6515	Remote Similarity	NPC605541
0.5902	Remote Similarity	NPC86485
0.5833	Remote Similarity	NPC44079
0.5645	Remote Similarity	NPC49824
0.5469	Remote Similarity	NPC99591
0.5397	Remote Similarity	NPC603348
0.5312	Remote Similarity	NPC54394
0.5312	Remote Similarity	NPC159103
0.5238	Remote Similarity	NPC276905
0.5238	Remote Similarity	NPC281207
0.5238	Remote Similarity	NPC605146
0.5152	Remote Similarity	NPC9117
0.5079	Remote Similarity	NPC152042
0.5077	Remote Similarity	NPC200740
0.5077	Remote Similarity	NPC166753
0.5067	Remote Similarity	NPC244407

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC572083 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4189
0.1-0.2	4856
0.2-0.3	100
0.3-0.4	3
0.4-0.5	1
0.5-0.6	0
0.6-0.7	0
0.7-0.8	1
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7049	Intermediate Similarity	NPD4378	Phase 3

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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