NPASS Compound

Natural Product: NPC558394

Natural Product ID	NPC558394
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	5'-Hydroxymorin
IUPAC Name	3,5,7-trihydroxy-2-(2,4,5-trihydroxyphenyl)chromen-4-one
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001615] Flavones [CHEMONTID:0001136] Flavonols

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 33 35 0 0 0 0 0 0 0 0999 V2000 2.3016 -2.7192 0.9258 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7618 -1.6521 0.5348 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3530 -1.5785 0.6115 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3393 -2.6591 1.0928 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2463 -0.4498 0.2020 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6623 -0.1835 0.1985 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1232 0.8676 -0.6118 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4472 1.2233 -0.6425 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8888 2.2725 -1.4553 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3934 0.5732 0.1154 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7214 0.9593 0.0581 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9772 -0.4555 0.9169 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6123 -0.8120 0.9409 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2736 -1.8517 1.7790 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5157 0.5642 -0.2670 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7992 0.5435 -0.3566 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5186 1.6349 -0.8535 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8706 1.5371 -0.9168 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5947 2.6215 -1.4111 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5601 0.4058 -0.5110 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8575 -0.6548 -0.0280 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4673 -1.8448 0.4076 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4790 -0.5872 0.0496 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2137 -3.5975 0.7602 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4282 1.4091 -1.2272 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5185 2.1039 -2.2458 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0789 1.7989 0.5010 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6758 -1.0042 1.5358 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7594 -1.9562 2.6614 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9436 2.4955 -1.1583 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0906 3.2328 -0.7742 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6368 0.3638 -0.5760 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6095 -2.6007 -0.2562 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 1 0 3 5 2 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 1 0 8 10 2 0 10 11 1 0 10 12 1 0 12 13 2 0 13 14 1 0 5 15 1 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 1 0 18 20 2 0 20 21 1 0 21 22 1 0 21 23 2 0 23 2 1 0 13 6 1 0 23 16 1 0 4 24 1 0 7 25 1 0 9 26 1 0 11 27 1 0 12 28 1 0 14 29 1 0 17 30 1 0 19 31 1 0 20 32 1 0 22 33 1 0 M END

Standard InCHIKey	GCWMEFUMPZHUFF-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C15H10O8/c16-5-1-10(20)12-11(2-5)23-15(14(22)13(12)21)6-3-8(18)9(19)4-7(6)17/h1-4,16-20,22H
SMILES	O=C1C(O)=C(C2=CC(O)=C(O)C=C2O)OC2=CC(O)=CC(O)=C12

Calculated Properties

Physi-Chem Properties

Molecular Weight:	318.04	Volume:	291.557 ? Van der Waals volume.
Dense:	1.091	LogP:	1.001 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.089 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.377 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	1.0	Rigid Bonds:	18.0
TPSA:	151.59 ? Topological Polar Surface Area.	H-Bond Acceptor:	8.0
H-Bond Donor:	6.0	Rings:	3.0
Heavy Atoms:	8.0

MedChem Properties

QED Drug-Likeness Score:	0.293	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.768	Fsp³:	0.0
MCE-18:	20.0 ? 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:	Rejected
Golden Triangle Rule:	Rejected	BMS Rule:	1
Chelating Alert:	1	PAINS Alert:	1
Colloidal aggregators:	0.894	Fluc inhibitor:	0.354 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.787 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.174 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.715	Promiscuous compounds:	0.923

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.445	MDCK Permeability:	-4.907
Pgp-inhibitor:	0.025	Pgp-substrate:	0.143
PAMPA:	0.74 ? 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):	0.073
20% Bioavailability (F20%):	0.355	30% Bioavailability (F30%):	0.987
50% Bioavailability (F50%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.914
Plasma Protein Binding (PPB):	97.942%	Volume Distribution (VD):	-0.826
Fu:	1.57% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.86
OATP1B3 inhibitor:	0.995	BCRP inhibitor:	0.993
BSEP inhibitor:	0.201

ADMET: Metabolism

CYP1A2-inhibitor:	0.124	CYP1A2-substrate:	0.009
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.148
CYP2C9-inhibitor:	0.077	CYP2C9-substrate:	0.003
CYP2D6-inhibitor:	0.984	CYP2D6-substrate:	0.843
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.001
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.983 ? 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):

6.591

Half-life (T1/2):

2.007

ADMET: Toxicity

hERG Blockers:	0.037	hERG Blockers (10um):	0.535
Human Hepatotoxicity (H-HT):	0.348	Drug-induced Liver Injury (DILI):	0.668
AMES Toxicity:	0.591	Rat Oral Acute Toxicity:	0.491
Maximum Recommended Daily Dose:	0.822	Skin Sensitization:	0.921
Carcinogencity:	0.516	Eye Corrosion:	0.395
Eye Irritation:	0.999	Respiratory Toxicity:	0.745
Drug-induced Neurotoxicity:	0.004	Ototoxicity:	0.163
Hematotoxicity:	0.025	Drug-induced Nephrotoxicity:	0.011
Genotoxicity:	0.977	RPMI-8226 Immunitoxicity:	0.033
A549 Cytotoxicity:	0.721	Hek293 Cytotoxicity:	0.662
BCF:	1.08 ? 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:	3.64 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.432 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.92 ? 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
NPO28036	Distemonanthus benthamianus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO27000	Geranium macrorrhizum	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO28036	Distemonanthus benthamianus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28036	Distemonanthus benthamianus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28036	Distemonanthus benthamianus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27000	Geranium macrorrhizum	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28036	Distemonanthus benthamianus	Species	Fabaceae	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 NPC558394 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	40233
0.1-0.2	7896
0.2-0.3	1243
0.3-0.4	406
0.4-0.5	60
0.5-0.6	12
0.6-0.7	5
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
0.7143	Intermediate Similarity	NPC20791
0.7	Intermediate Similarity	NPC179271
0.7	Intermediate Similarity	NPC216361
0.6863	Remote Similarity	NPC256042
0.68	Remote Similarity	NPC169749
0.6471	Remote Similarity	NPC601197
0.6275	Remote Similarity	NPC116775
0.6275	Remote Similarity	NPC187432
0.5893	Remote Similarity	NPC50403
0.5763	Remote Similarity	NPC133953
0.5714	Remote Similarity	NPC219330
0.569	Remote Similarity	NPC54394
0.5614	Remote Similarity	NPC241838
0.5614	Remote Similarity	NPC28274
0.5593	Remote Similarity	NPC609179
0.5424	Remote Similarity	NPC159103
0.5397	Remote Similarity	NPC205046
0.5246	Remote Similarity	NPC125062
0.5179	Remote Similarity	NPC279121
0.5091	Remote Similarity	NPC77858

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC558394 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7955
0.1-0.2	1170
0.2-0.3	20
0.3-0.4	3
0.4-0.5	0
0.5-0.6	1
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
0.7143	Intermediate Similarity	NPD1512	Phase 3
0.5179	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