NPASS Compound

Natural Product: NPC502176

Natural Product ID	NPC502176
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	3-[4-[(2~{S},3~{S},4~{R})-3,4-dihydroxy-4-(hydroxymethyl)tetrahydrofuran-2-yl]oxyphenyl]-7-[(2~{S},3~{R},4~{S},5~{S},6~{S})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-chromen-4-one
IUPAC Name	3-[4-[(2~{S},3~{S},4~{R})-3,4-dihydroxy-4-(hydroxymethyl)tetrahydrofuran-2-yl]oxyphenyl]-7-[(2~{S},3~{R},4~{S},5~{S},6~{S})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-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 67 71 0 0 0 0 0 0 0 0999 V2000 -0.8249 -0.5550 -1.4922 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1468 -0.3146 -0.4649 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7704 -0.0267 0.7306 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2227 0.0062 0.8307 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9694 0.6464 -0.1335 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3525 0.7097 -0.0880 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0423 0.1281 0.9353 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4150 0.1636 1.0253 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.3069 0.7509 0.1611 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.9834 1.7686 0.8228 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.1881 1.9455 0.1634 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5692 0.6669 -0.4924 C 0 0 2 0 0 0 0 0 0 0 0 0 -9.8678 0.8707 -1.8408 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.7790 0.0810 0.2072 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.5435 -0.1423 1.5432 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.3600 -0.1894 -0.3724 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.5423 -1.2704 0.4959 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2882 -0.5267 1.9224 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9177 -0.5771 1.8571 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0513 0.2247 1.8078 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3661 0.1924 1.7033 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9922 -0.0770 0.5850 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3800 -0.1050 0.5003 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0764 -0.3825 -0.6509 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4446 -0.4191 -0.7729 O 0 0 0 0 0 0 0 0 0 0 0 0 6.3500 -0.1833 0.2506 C 0 0 2 0 0 0 0 0 0 0 0 0 7.1719 0.8936 0.0570 O 0 0 0 0 0 0 0 0 0 0 0 0 8.2738 0.7430 -0.6936 C 0 0 1 0 0 0 0 0 0 0 0 0 9.2711 1.8405 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0 10.4331 1.7503 -1.0452 O 0 0 0 0 0 0 0 0 0 0 0 0 8.9874 -0.5509 -0.6384 C 0 0 1 0 0 0 0 0 0 0 0 0 9.7258 -0.6850 0.5482 O 0 0 0 0 0 0 0 0 0 0 0 0 8.0111 -1.7084 -0.6618 C 0 0 2 0 0 0 0 0 0 0 0 0 7.2890 -1.7527 -1.8526 O 0 0 0 0 0 0 0 0 0 0 0 0 7.0834 -1.4806 0.5021 C 0 0 1 0 0 0 0 0 0 0 0 0 7.7872 -1.4772 1.6811 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2702 -0.6462 -1.7784 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8990 -0.6251 -1.7220 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2457 -0.3404 -0.5401 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4251 1.1136 -0.9544 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8314 1.2423 -0.9052 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7868 1.2248 -0.6862 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.0688 2.7271 -0.6154 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.9343 2.3416 0.8821 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.9270 -0.0296 -2.2730 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.1855 -0.7932 -0.3384 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.5849 0.8669 0.1540 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.0440 -0.9299 1.8308 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0304 -0.5216 -1.3734 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.3691 -1.7529 0.3209 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8621 -0.9780 2.7204 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3580 -1.0866 2.6285 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3953 0.4533 2.7586 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9001 0.1123 1.4242 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8073 0.0227 1.1880 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0183 0.9571 -1.7678 H 0 0 0 0 0 0 0 0 0 0 0 0 9.5465 1.7675 0.7670 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8362 2.8450 -0.4469 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3148 1.4935 -1.9733 H 0 0 0 0 0 0 0 0 0 0 0 0 9.6803 -0.5963 -1.5248 H 0 0 0 0 0 0 0 0 0 0 0 0 10.0450 -1.6281 0.5786 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5800 -2.6228 -0.4743 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4572 -0.9137 -2.3678 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3268 -2.2901 0.5364 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2221 -1.1299 2.4231 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7794 -0.8704 -2.7086 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2692 -0.8260 -2.5811 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 4 5 2 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 6 12 14 1 0 14 15 1 0 12 16 1 0 16 17 1 0 7 18 1 0 18 19 2 0 3 20 2 0 20 21 1 0 21 22 1 0 22 23 2 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 28 31 1 0 31 32 1 0 31 33 1 0 33 34 1 0 33 35 1 0 35 36 1 0 24 37 2 0 37 38 1 0 38 39 2 0 39 2 1 0 19 4 1 0 39 22 1 0 16 9 1 0 35 26 1 0 5 40 1 0 6 41 1 0 9 42 1 6 11 43 1 0 11 44 1 0 13 45 1 0 14 46 1 0 14 47 1 0 15 48 1 0 16 49 1 6 17 50 1 0 18 51 1 0 19 52 1 0 20 53 1 0 23 54 1 0 26 55 1 1 28 56 1 6 29 57 1 0 29 58 1 0 30 59 1 0 31 60 1 6 32 61 1 0 33 62 1 1 34 63 1 0 35 64 1 1 36 65 1 0 37 66 1 0 38 67 1 0 M END

Standard InCHIKey	CLSSVAPYJUYEAY-WJAPLXOZSA-N
Standard InCHI	InChI=1S/C26H28O13/c27-8-18-20(30)21(31)22(32)24(39-18)38-14-5-6-15-17(7-14)35-9-16(19(15)29)12-1-3-13(4-2-12)37-25-23(33)26(34,10-28)11-36-25/h1-7,9,18,20-25,27-28,30-34H,8,10-11H2/t18-,20+,21-,22+,23+,24+,25-,26+/m0/s1
SMILES	O=C1C(C2=CC=C(O[C@@H]3OC[C@](O)(CO)[C@@H]3O)C=C2)=COC2=CC(O[C@@H]3O[C@@H](CO)[C@@H](O)[C@H](O)[C@H]3O)=CC=C12

Calculated Properties

Physi-Chem Properties

Molecular Weight:	548.15	Volume:	508.651 ? Van der Waals volume.
Dense:	1.078	LogP:	0.887 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.413 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.873 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	7.0	Rigid Bonds:	29.0
TPSA:	208.74 ? Topological Polar Surface Area.	H-Bond Acceptor:	13.0
H-Bond Donor:	7.0	Rings:	5.0
Heavy Atoms:	13.0

MedChem Properties

QED Drug-Likeness Score:	0.179	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.492	Fsp³:	0.423
MCE-18:	111.568 ? 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:	0	PAINS Alert:	0
Colloidal aggregators:	0.566	Fluc inhibitor:	0.364 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.858 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.385 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.115	Promiscuous compounds:	0.145

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.627	MDCK Permeability:	-5.128
Pgp-inhibitor:	0.0	Pgp-substrate:	0.169
PAMPA:	1.0 ? 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):	0.971
20% Bioavailability (F20%):	0.973	30% Bioavailability (F30%):	0.985
50% Bioavailability (F50%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001	MRP1:	0.551
Plasma Protein Binding (PPB):	80.823%	Volume Distribution (VD):	-0.224
Fu:	22.644% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.837
OATP1B3 inhibitor:	0.963	BCRP inhibitor:	0.018
BSEP inhibitor:	0.003

ADMET: Metabolism

CYP1A2-inhibitor:	0.005	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.002	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.974
HLM stability:	0.0 ? 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):

1.725

Half-life (T1/2):

2.62

ADMET: Toxicity

hERG Blockers:	0.026	hERG Blockers (10um):	0.052
Human Hepatotoxicity (H-HT):	0.909	Drug-induced Liver Injury (DILI):	0.988
AMES Toxicity:	0.993	Rat Oral Acute Toxicity:	0.11
Maximum Recommended Daily Dose:	0.026	Skin Sensitization:	0.999
Carcinogencity:	0.484	Eye Corrosion:	0.0
Eye Irritation:	0.078	Respiratory Toxicity:	0.013
Drug-induced Neurotoxicity:	0.059	Ototoxicity:	0.982
Hematotoxicity:	0.675	Drug-induced Nephrotoxicity:	0.989
Genotoxicity:	0.93	RPMI-8226 Immunitoxicity:	0.289
A549 Cytotoxicity:	0.841	Hek293 Cytotoxicity:	0.345
BCF:	0.74 ? 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:	3.396 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.909 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.172 ? 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
NPO54916	Neorautanenia amboensis	Species	Fabaceae	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 NPC502176 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	22019
0.1-0.2	24520
0.2-0.3	2615
0.3-0.4	595
0.4-0.5	75
0.5-0.6	21
0.6-0.7	9
0.7-0.8	1
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
0.8	Intermediate Similarity	NPC45165
0.7342	Intermediate Similarity	NPC161749
0.7143	Intermediate Similarity	NPC25547
0.6988	Remote Similarity	NPC229729
0.6988	Remote Similarity	NPC601607
0.6707	Remote Similarity	NPC258035
0.6667	Remote Similarity	NPC135345
0.6489	Remote Similarity	NPC235575
0.6429	Remote Similarity	NPC73511
0.619	Remote Similarity	NPC211014
0.6118	Remote Similarity	NPC156457
0.6118	Remote Similarity	NPC603782
0.5765	Remote Similarity	NPC487214
0.5747	Remote Similarity	NPC197896
0.5747	Remote Similarity	NPC105511
0.5747	Remote Similarity	NPC313163
0.567	Remote Similarity	NPC51326
0.5568	Remote Similarity	NPC234739
0.5517	Remote Similarity	NPC160515
0.5495	Remote Similarity	NPC43761
0.5444	Remote Similarity	NPC100720
0.5444	Remote Similarity	NPC205076
0.5435	Remote Similarity	NPC307518
0.54	Remote Similarity	NPC231194
0.5258	Remote Similarity	NPC479405
0.5217	Remote Similarity	NPC479402
0.5204	Remote Similarity	NPC479404
0.5109	Remote Similarity	NPC138540
0.5055	Remote Similarity	NPC168822
0.5054	Remote Similarity	NPC224462
0.5054	Remote Similarity	NPC80140
0.5053	Remote Similarity	NPC48773
0.5053	Remote Similarity	NPC479407

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC502176 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4900
0.1-0.2	4164
0.2-0.3	74
0.3-0.4	9
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
0.7342	Intermediate Similarity	NPD4381	Clinical (unspecified phase)

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