NPASS Compound

Natural Product: NPC8670

Natural Product ID	NPC8670
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	WYUFTYLVLQZQNH-HNEXDWKRSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	9859136
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0002207] O-glycosyl 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 30 30 0 0 0 0 0 0 0 0999 V2000 2.7919 1.8689 -1.6415 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5693 0.9485 -0.4531 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2864 0.5162 -0.4805 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9020 -0.3349 0.5301 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4912 -1.6953 0.0896 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9679 -1.7013 -0.2192 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.5608 -0.3370 -0.4300 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.1483 0.6696 0.5828 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.2905 1.1322 1.4621 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9028 2.1763 2.3003 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0683 0.2115 1.3660 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9657 -0.4534 -0.3671 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7237 -2.3216 0.7863 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2036 -2.1900 -0.9834 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4965 2.6825 -1.3283 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2282 1.3363 -2.5030 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8310 2.3703 -1.8902 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3462 0.1666 -0.5197 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7141 1.5642 0.4814 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8099 -0.4739 1.1752 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6390 -2.3882 0.9697 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1357 -2.3016 -1.1350 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3156 -0.0059 -1.4588 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7712 1.5687 0.0533 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6648 0.3254 2.1333 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1334 1.4900 0.8388 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0749 2.5642 1.8709 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2957 -0.9602 -1.1574 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3864 -3.2460 0.8971 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0962 -3.1826 -0.9697 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 8 11 1 0 7 12 1 0 6 13 1 0 5 14 1 0 11 4 1 0 1 15 1 0 1 16 1 0 1 17 1 0 2 18 1 0 2 19 1 0 4 20 1 1 5 21 1 1 6 22 1 6 7 23 1 6 8 24 1 6 9 25 1 0 9 26 1 0 10 27 1 0 12 28 1 0 13 29 1 0 14 30 1 0 M END

Standard InCHIKey	WYUFTYLVLQZQNH-HNEXDWKRSA-N
Standard InCHI	InChI=1S/C8H16O6/c1-2-13-8-7(12)6(11)5(10)4(3-9)14-8/h4-12H,2-3H2,1H3/t4-,5+,6+,7-,8+/m1/s1
SMILES	CCO[C@@H]1[C@@H]([C@H]([C@H]([C@@H](CO)O1)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	208.09	Volume:	191.109 ? Van der Waals volume.
Dense:	1.089	LogP:	-1.508 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-1.326 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	0.031 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	3.0	Rigid Bonds:	6.0
TPSA:	99.38 ? Topological Polar Surface Area.	H-Bond Acceptor:	6.0
H-Bond Donor:	4.0	Rings:	1.0
Heavy Atoms:	6.0

MedChem Properties

QED Drug-Likeness Score:	0.421	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.503	Fsp³:	1.0
MCE-18:	21.0 ? 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:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.185	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.038 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.0 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.524	Promiscuous compounds:	0.067

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.76	MDCK Permeability:	-4.942
Pgp-inhibitor:	0.0	Pgp-substrate:	0.57
PAMPA:	0.995 ? 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):	0.616
20% Bioavailability (F20%):	0.683	30% Bioavailability (F30%):	0.688
50% Bioavailability (F50%):	0.874

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.003	MRP1:	0.634
Plasma Protein Binding (PPB):	23.444%	Volume Distribution (VD):	-0.465
Fu:	77.329% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.138
OATP1B3 inhibitor:	0.126	BCRP inhibitor:	0.006
BSEP inhibitor:	0.011

ADMET: Metabolism

CYP1A2-inhibitor:	0.107	CYP1A2-substrate:	0.001
CYP2C19-inhibitor:	0.194	CYP2C19-substrate:	0.015
CYP2C9-inhibitor:	0.108	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.001	CYP2D6-substrate:	0.008
CYP3A4-inhibitor:	0.03	CYP3A4-substrate:	0.291
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.253
HLM stability:	0.526 ? 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):

2.247

Half-life (T1/2):

2.279

ADMET: Toxicity

hERG Blockers:	0.026	hERG Blockers (10um):	0.248
Human Hepatotoxicity (H-HT):	0.384	Drug-induced Liver Injury (DILI):	0.468
AMES Toxicity:	0.91	Rat Oral Acute Toxicity:	0.141
Maximum Recommended Daily Dose:	0.041	Skin Sensitization:	0.995
Carcinogencity:	0.416	Eye Corrosion:	0.081
Eye Irritation:	0.944	Respiratory Toxicity:	0.232
Drug-induced Neurotoxicity:	0.076	Ototoxicity:	0.696
Hematotoxicity:	0.552	Drug-induced Nephrotoxicity:	0.578
Genotoxicity:	0.111	RPMI-8226 Immunitoxicity:	0.076
A549 Cytotoxicity:	0.331	Hek293 Cytotoxicity:	0.114
BCF:	0.197 ? 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:	1.619 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	2.85 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	2.118 ? 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
NPO31494	Acanthopanax senticosus	n.a.	n.a.	n.a.	n.a.	leaf	n.a.	PMID[11816040]
NPO31494	Acanthopanax senticosus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[17125224]
NPO31494	Acanthopanax senticosus	n.a.	n.a.	n.a.	Barks	Iksan, Chunbuk, Korea	n.a.	PMID[3127544]
NPO31494	Acanthopanax senticosus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO31494	Acanthopanax senticosus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO31494	Acanthopanax senticosus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCM_Taiwan]

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 NPC8670 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	26690
0.1-0.2	18818
0.2-0.3	3382
0.3-0.4	702
0.4-0.5	209
0.5-0.6	31
0.6-0.7	15
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC124963
0.7667	Intermediate Similarity	NPC326533
0.7273	Intermediate Similarity	NPC233726
0.7241	Intermediate Similarity	NPC23134
0.6897	Remote Similarity	NPC42503
0.6897	Remote Similarity	NPC282143
0.6897	Remote Similarity	NPC107914
0.6897	Remote Similarity	NPC242073
0.6897	Remote Similarity	NPC299781
0.6897	Remote Similarity	NPC157193
0.6897	Remote Similarity	NPC608193
0.6857	Remote Similarity	NPC155457
0.6486	Remote Similarity	NPC13143
0.6486	Remote Similarity	NPC294813
0.6486	Remote Similarity	NPC606861
0.6486	Remote Similarity	NPC607126
0.6216	Remote Similarity	NPC145112
0.6176	Remote Similarity	NPC143326
0.6	Remote Similarity	NPC31496
0.5946	Remote Similarity	NPC268243
0.5882	Remote Similarity	NPC317501
0.5882	Remote Similarity	NPC605930
0.575	Remote Similarity	NPC89145
0.575	Remote Similarity	NPC157514
0.575	Remote Similarity	NPC322314
0.575	Remote Similarity	NPC269166
0.5714	Remote Similarity	NPC147292
0.561	Remote Similarity	NPC100204
0.5581	Remote Similarity	NPC277570
0.5581	Remote Similarity	NPC63058
0.5476	Remote Similarity	NPC36927
0.5476	Remote Similarity	NPC262826
0.5476	Remote Similarity	NPC271772
0.5455	Remote Similarity	NPC323574
0.5455	Remote Similarity	NPC206601
0.5349	Remote Similarity	NPC150557
0.5263	Remote Similarity	NPC130683
0.525	Remote Similarity	NPC603514
0.5227	Remote Similarity	NPC306255
0.5217	Remote Similarity	NPC12040
0.5116	Remote Similarity	NPC166250
0.5111	Remote Similarity	NPC157338
0.5111	Remote Similarity	NPC34877
0.5106	Remote Similarity	NPC280367
0.5106	Remote Similarity	NPC71381
0.5106	Remote Similarity	NPC285003
0.5106	Remote Similarity	NPC9447
0.5106	Remote Similarity	NPC470124
0.5106	Remote Similarity	NPC263407
0.5102	Remote Similarity	NPC137368

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC8670 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7268
0.1-0.2	1679
0.2-0.3	168
0.3-0.4	14
0.4-0.5	8
0.5-0.6	5
0.6-0.7	1
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
0.6765	Remote Similarity	NPD904	Phase 3
0.5806	Remote Similarity	NPD8994	Approved
0.5714	Remote Similarity	NPD905	Phase 4
0.5263	Remote Similarity	NPD887	Approved
0.5263	Remote Similarity	NPD895	Phase 4
0.5227	Remote Similarity	NPD3181	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