NPASS Compound

Natural Product: NPC524982

Natural Product ID	NPC524982
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Ochnaflavone-7"-O-methyl ether
IUPAC Name	5,7-dihydroxy-2-[4-hydroxy-3-[4-(5-hydroxy-7-methoxy-4-oxo-chromen-2-yl)phenoxy]phenyl]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 61 66 0 0 0 0 0 0 0 0999 V2000 10.9130 -0.5151 -0.0769 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5764 -0.8777 -0.3027 O 0 0 0 0 0 0 0 0 0 0 0 0 8.5701 -0.1806 0.3373 C 0 0 0 0 0 0 0 0 0 0 0 0 8.8898 0.8700 1.1961 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8314 1.5184 1.7985 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0643 2.5873 2.6775 O 0 0 0 0 0 0 0 0 0 0 0 0 6.5146 1.1435 1.5613 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4525 1.7861 2.1590 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6578 2.7492 2.9513 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1690 1.3475 1.8668 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9079 0.3012 1.0083 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5635 -0.1752 0.6880 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4430 -1.2323 -0.1876 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2424 -1.7768 -0.5730 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0837 -1.2378 -0.0569 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1248 -1.7581 -0.4245 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9917 -1.2603 -1.3861 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2897 -0.8851 -1.0129 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2149 -0.3819 -1.9014 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5568 -0.0029 -1.4719 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5361 0.5027 -2.2801 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8068 0.8475 -1.8038 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6818 1.3110 -2.5837 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.0395 0.6548 -0.4638 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.2753 0.9789 0.0545 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.2972 1.4986 -0.7504 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.4886 0.7784 1.3996 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.4921 0.2653 2.2154 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.7658 0.0834 3.5726 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.2765 -0.0436 1.6571 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0231 0.1424 0.3144 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8505 -0.1626 -0.1891 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7968 -0.2606 -3.2080 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5152 -0.6269 -3.5968 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5966 -1.1309 -2.6930 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3087 -1.4935 -3.1094 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1915 -0.1640 0.8337 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4110 0.3617 1.2026 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9746 -0.2706 0.4694 O 0 0 0 0 0 0 0 0 0 0 0 0 6.2058 0.1030 0.7104 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2603 -0.5451 0.1085 C 0 0 0 0 0 0 0 0 0 0 0 0 11.1589 0.4377 -0.5811 H 0 0 0 0 0 0 0 0 0 0 0 0 11.1298 -0.4303 0.9983 H 0 0 0 0 0 0 0 0 0 0 0 0 11.5632 -1.3256 -0.5111 H 0 0 0 0 0 0 0 0 0 0 0 0 9.9047 1.1577 1.3778 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8996 2.6381 3.2444 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3318 1.8526 2.3367 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3610 -1.6698 -0.6058 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2825 -2.6150 -1.2613 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6055 -0.9854 0.0163 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3239 0.6426 -3.3268 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.7409 0.9120 -1.4633 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.4434 1.0153 1.8662 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0082 -0.3025 4.1541 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5126 -0.4422 2.3079 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5053 0.1340 -3.9340 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2059 -0.5239 -4.6281 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0784 -2.4706 -3.2729 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7400 0.2511 1.2339 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4793 1.2020 1.9005 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0591 -1.3623 -0.5622 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 1 0 5 7 2 0 7 8 1 0 8 9 2 0 8 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 22 24 1 0 24 25 2 0 25 26 1 0 25 27 1 0 27 28 2 0 28 29 1 0 28 30 1 0 30 31 2 0 31 32 1 0 19 33 2 0 33 34 1 0 34 35 2 0 35 36 1 0 15 37 1 0 37 38 2 0 11 39 1 0 39 40 1 0 40 41 2 0 41 3 1 0 40 7 1 0 38 12 1 0 35 17 1 0 32 20 1 0 31 24 1 0 1 42 1 0 1 43 1 0 1 44 1 0 4 45 1 0 6 46 1 0 10 47 1 0 13 48 1 0 14 49 1 0 18 50 1 0 21 51 1 0 26 52 1 0 27 53 1 0 29 54 1 0 30 55 1 0 33 56 1 0 34 57 1 0 36 58 1 0 37 59 1 0 38 60 1 0 41 61 1 0 M END

Standard InCHIKey	PMCJZCZORABGEL-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C31H20O10/c1-38-19-11-22(35)31-23(36)13-25(40-29(31)12-19)15-2-5-18(6-3-15)39-27-8-16(4-7-20(27)33)26-14-24(37)30-21(34)9-17(32)10-28(30)41-26/h2-14,32-35H,1H3
SMILES	COC1=CC(O)=C2C(=O)C=C(C3=CC=C(OC4=CC(C5=CC(=O)C6=C(O)C=C(O)C=C6O5)=CC=C4O)C=C3)OC2=C1

Calculated Properties

Physi-Chem Properties

Molecular Weight:	552.11	Volume:	539.112 ? Van der Waals volume.
Dense:	1.024	LogP:	4.486 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.017 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-6.121 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	5.0	Rigid Bonds:	36.0
TPSA:	159.8 ? Topological Polar Surface Area.	H-Bond Acceptor:	10.0
H-Bond Donor:	4.0	Rings:	6.0
Heavy Atoms:	10.0

MedChem Properties

QED Drug-Likeness Score:	0.204	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.889	Fsp³:	0.032
MCE-18:	35.0 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.996	Fluc inhibitor:	0.787 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.984 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.996 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.492	Promiscuous compounds:	0.883

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.985	MDCK Permeability:	-4.791
Pgp-inhibitor:	0.07	Pgp-substrate:	0.119
PAMPA:	0.182 ? 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):	0.002
20% Bioavailability (F20%):	0.423	30% Bioavailability (F30%):	0.927
50% Bioavailability (F50%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.89
Plasma Protein Binding (PPB):	97.38%	Volume Distribution (VD):	-0.266
Fu:	1.887% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.993
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.997
BSEP inhibitor:	0.995

ADMET: Metabolism

CYP1A2-inhibitor:	0.785	CYP1A2-substrate:	0.948
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.001
CYP2C9-inhibitor:	0.993	CYP2C9-substrate:	0.995
CYP2D6-inhibitor:	1.0	CYP2D6-substrate:	1.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.561
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.927 ? 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):

2.629

Half-life (T1/2):

1.523

ADMET: Toxicity

hERG Blockers:	0.135	hERG Blockers (10um):	0.584
Human Hepatotoxicity (H-HT):	0.42	Drug-induced Liver Injury (DILI):	0.991
AMES Toxicity:	0.823	Rat Oral Acute Toxicity:	0.537
Maximum Recommended Daily Dose:	0.978	Skin Sensitization:	0.277
Carcinogencity:	0.908	Eye Corrosion:	0.006
Eye Irritation:	0.997	Respiratory Toxicity:	0.892
Drug-induced Neurotoxicity:	0.004	Ototoxicity:	0.051
Hematotoxicity:	0.037	Drug-induced Nephrotoxicity:	0.01
Genotoxicity:	0.998	RPMI-8226 Immunitoxicity:	0.076
A549 Cytotoxicity:	0.656	Hek293 Cytotoxicity:	0.963
BCF:	1.328 ? 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:	4.576 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.129 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.814 ? 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
NPO54770	Ochna pumila	Genus	Ochnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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 NPC524982 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	30676
0.1-0.2	16375
0.2-0.3	1719
0.3-0.4	811
0.4-0.5	220
0.5-0.6	37
0.6-0.7	14
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8209	Intermediate Similarity	NPC112954
0.6757	Remote Similarity	NPC183
0.6667	Remote Similarity	NPC272064
0.6538	Remote Similarity	NPC600396
0.6479	Remote Similarity	NPC183950
0.6479	Remote Similarity	NPC137062
0.6377	Remote Similarity	NPC231772
0.6377	Remote Similarity	NPC234133
0.6232	Remote Similarity	NPC29353
0.6111	Remote Similarity	NPC195202
0.6111	Remote Similarity	NPC219927
0.6111	Remote Similarity	NPC12200
0.6111	Remote Similarity	NPC611172
0.6104	Remote Similarity	NPC34089
0.6104	Remote Similarity	NPC196179
0.5976	Remote Similarity	NPC121649
0.5904	Remote Similarity	NPC601565
0.589	Remote Similarity	NPC52005
0.589	Remote Similarity	NPC223579
0.5854	Remote Similarity	NPC194593
0.5833	Remote Similarity	NPC108406
0.5833	Remote Similarity	NPC265624
0.5775	Remote Similarity	NPC127447
0.5732	Remote Similarity	NPC303485
0.5714	Remote Similarity	NPC205026
0.5698	Remote Similarity	NPC55443
0.5694	Remote Similarity	NPC483773
0.561	Remote Similarity	NPC600972
0.5595	Remote Similarity	NPC215203
0.5542	Remote Similarity	NPC290830
0.5542	Remote Similarity	NPC158027
0.5529	Remote Similarity	NPC18699
0.5507	Remote Similarity	NPC50898
0.5479	Remote Similarity	NPC33265
0.5479	Remote Similarity	NPC48479
0.5479	Remote Similarity	NPC62536
0.5479	Remote Similarity	NPC120464
0.5479	Remote Similarity	NPC601901
0.5476	Remote Similarity	NPC159707
0.5476	Remote Similarity	NPC14606
0.5476	Remote Similarity	NPC186227
0.5467	Remote Similarity	NPC124784
0.5467	Remote Similarity	NPC177298
0.5467	Remote Similarity	NPC606638
0.5455	Remote Similarity	NPC605634
0.5422	Remote Similarity	NPC603508
0.5357	Remote Similarity	NPC71061
0.5357	Remote Similarity	NPC72425
0.5238	Remote Similarity	NPC150908
0.5139	Remote Similarity	NPC279121
0.5119	Remote Similarity	NPC248739
0.507	Remote Similarity	NPC78540

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC524982 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5970
0.1-0.2	3119
0.2-0.3	51
0.3-0.4	6
0.4-0.5	3
0.5-0.6	1
0.6-0.7	0
0.7-0.8	0
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
0.5139	Remote Similarity	NPD1511	Phase 2

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