NPASS Compound

Natural Product: NPC485026

Natural Product ID	NPC485026
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	NVLAJKWLQGAHLT-JAZPPYFYSA-N
IUPAC Name	n.a.
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 75 74 0 0 0 0 0 0 0 0999 V2000 -8.5938 0.3049 -3.1072 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4952 0.7118 -2.1554 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3289 -0.2468 -2.2653 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2152 0.1198 -1.3469 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5914 0.1258 0.1225 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0614 -1.2203 0.5787 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3757 -1.2573 2.0111 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3984 -1.3182 3.0756 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2118 -0.4602 3.2198 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0822 -0.7451 2.3009 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9363 0.2642 2.4686 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8818 -0.1936 1.4525 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3008 0.7795 1.5132 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3081 0.3108 0.5242 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4977 1.1867 0.4438 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2703 1.2633 1.7116 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7975 -0.0567 2.1405 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7387 -0.6945 1.1740 C 0 0 2 0 0 0 0 0 0 0 0 0 5.9196 0.2480 0.9620 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8510 -0.4354 -0.0059 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3085 -1.5765 0.2385 O 0 0 0 0 0 0 0 0 0 0 0 0 7.2102 0.1979 -1.1838 O 0 0 0 0 0 0 0 0 0 0 0 0 8.0923 -0.4437 -2.0984 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2240 0.5169 -3.2872 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1839 -0.0615 -4.3118 C 0 0 0 0 0 0 0 0 0 0 0 0 9.2650 0.8358 -5.3757 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9579 0.7008 -3.8417 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1781 -1.1136 -0.0143 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7432 0.7260 2.8115 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.3658 1.1037 -3.1272 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.1249 -0.5821 -2.6595 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1958 0.0868 -4.1125 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9318 0.7405 -1.1577 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1186 1.6993 -2.4853 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9195 -0.2325 -3.2969 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7342 -1.2609 -2.0951 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9097 1.1650 -1.5914 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3563 -0.5376 -1.4716 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8129 0.5802 0.6901 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4727 0.8774 0.2485 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9448 -1.5700 -0.0537 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2813 -2.0033 0.2927 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1182 -2.1328 2.1844 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1148 -0.3863 2.2676 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0027 -1.2206 4.0597 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0884 -2.4326 3.1526 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5324 0.6069 3.0262 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8504 -0.4842 4.2891 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5696 -1.7071 2.7240 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2518 -0.8853 1.2485 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5234 0.2214 3.4838 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2537 1.2734 2.1456 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4882 -1.1932 1.7265 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3191 -0.2693 0.4481 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1329 1.7691 1.2744 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6240 -0.7500 0.7868 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8561 0.2099 -0.5081 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1434 0.8854 -0.4266 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0995 2.2257 0.1949 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1191 2.0134 1.5928 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6769 1.7078 2.5467 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9473 -0.7553 2.3832 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3797 0.0970 3.0896 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1556 -1.6120 1.6766 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4567 0.3364 1.9204 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6098 1.2004 0.5274 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0885 -0.5760 -1.6153 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7130 -1.3886 -2.4930 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6026 1.4838 -2.9370 H 0 0 0 0 0 0 0 0 0 0 0 0 10.1834 -0.2062 -3.8880 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7927 -1.0151 -4.7189 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4978 0.8071 -5.9727 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3130 -0.0093 -3.5511 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7923 -1.0490 -0.7882 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6876 -0.1692 3.2143 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 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 2 0 20 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 24 27 1 0 18 28 1 0 13 29 1 0 1 30 1 0 1 31 1 0 1 32 1 0 2 33 1 0 2 34 1 0 3 35 1 0 3 36 1 0 4 37 1 0 4 38 1 0 5 39 1 0 5 40 1 0 6 41 1 0 6 42 1 0 7 43 1 0 7 44 1 0 8 45 1 0 8 46 1 0 9 47 1 0 9 48 1 0 10 49 1 0 10 50 1 0 11 51 1 0 11 52 1 0 12 53 1 0 12 54 1 0 13 55 1 6 14 56 1 0 14 57 1 0 15 58 1 0 15 59 1 0 16 60 1 0 16 61 1 0 17 62 1 0 17 63 1 0 18 64 1 1 19 65 1 0 19 66 1 0 23 67 1 0 23 68 1 0 24 69 1 0 25 70 1 0 25 71 1 0 26 72 1 0 27 73 1 0 28 74 1 0 29 75 1 0 M END

Standard InCHIKey	NVLAJKWLQGAHLT-JAZPPYFYSA-N
Standard InCHI	InChI=1S/C23H46O6/c1-2-3-4-5-6-7-8-9-10-11-14-20(25)15-12-13-16-21(26)17-23(28)29-19-22(27)18-24/h20-22,24-27H,2-19H2,1H3/t20-,21-,22?/m1/s1
SMILES	CCCCCCCCCCCC[C@H](CCCC[C@H](CC(=O)OCC(CO)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	418.33	Volume:	456.469 ? Van der Waals volume.
Dense:	0.916	LogP:	3.816 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.75 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.69 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	22.0	Rigid Bonds:	1.0
TPSA:	107.22 ? Topological Polar Surface Area.	H-Bond Acceptor:	6.0
H-Bond Donor:	4.0	Rings:	0.0
Heavy Atoms:	6.0

MedChem Properties

QED Drug-Likeness Score:	0.166	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.375	Fsp³:	0.957
MCE-18:	4.0 ? 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:	Rejected	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.399	Fluc inhibitor:	0.001 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.003 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.001 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.765	Promiscuous compounds:	0.088

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.183	MDCK Permeability:	-4.861
Pgp-inhibitor:	0.0	Pgp-substrate:	0.346
PAMPA:	0.347 ? 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):	0.574
20% Bioavailability (F20%):	0.991	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001	MRP1:	0.516
Plasma Protein Binding (PPB):	94.891%	Volume Distribution (VD):	0.288
Fu:	5.593% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.973
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.991
BSEP inhibitor:	0.363

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.004	CYP2C9-substrate:	0.039
CYP2D6-inhibitor:	0.054	CYP2D6-substrate:	0.215
CYP3A4-inhibitor:	0.092	CYP3A4-substrate:	0.998
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.984
HLM stability:	0.928 ? 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):

5.622

Half-life (T1/2):

0.737

ADMET: Toxicity

hERG Blockers:	0.061	hERG Blockers (10um):	0.527
Human Hepatotoxicity (H-HT):	0.672	Drug-induced Liver Injury (DILI):	0.003
AMES Toxicity:	0.046	Rat Oral Acute Toxicity:	0.005
Maximum Recommended Daily Dose:	0.469	Skin Sensitization:	0.998
Carcinogencity:	0.334	Eye Corrosion:	0.256
Eye Irritation:	0.988	Respiratory Toxicity:	0.603
Drug-induced Neurotoxicity:	0.014	Ototoxicity:	0.957
Hematotoxicity:	0.113	Drug-induced Nephrotoxicity:	0.928
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.022
A549 Cytotoxicity:	0.263	Hek293 Cytotoxicity:	0.015
BCF:	1.6 ? 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:	4.765 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.959 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.417 ? 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
NPO40913	Propolis resin	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[31429567]

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

Activity Type	# Activity
Inhibition	3

Activity Type	# Activity
Cell line	3

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
NPT579	Cell line	DLD-1	Homo sapiens	Inhibition	=	80.0	%	PMID[31429567]
NPT465	Cell line	NCI-N87	Homo sapiens	Inhibition	=	100.0	%	PMID[31429567]
NPT23301	Cell line	KYSE-30	Homo sapiens	Inhibition	=	52.0	%	PMID[31429567]

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 NPC485026 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	17067
0.1-0.2	29112
0.2-0.3	3151
0.3-0.4	471
0.4-0.5	39
0.5-0.6	8
0.6-0.7	2
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	Natural Product ID
0.7297	Intermediate Similarity	NPC485027
0.7297	Intermediate Similarity	NPC485028
0.7059	Intermediate Similarity	NPC488257
0.7059	Intermediate Similarity	NPC469937
0.7059	Intermediate Similarity	NPC94699
0.7059	Intermediate Similarity	NPC320588
0.7059	Intermediate Similarity	NPC53463
0.6111	Remote Similarity	NPC106872
0.6	Remote Similarity	NPC104537
0.5714	Remote Similarity	NPC476654
0.5714	Remote Similarity	NPC476655
0.5714	Remote Similarity	NPC476656
0.5641	Remote Similarity	NPC609455
0.5581	Remote Similarity	NPC330426
0.5581	Remote Similarity	NPC127091
0.5581	Remote Similarity	NPC22101
0.5349	Remote Similarity	NPC321919

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC485026 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6064
0.1-0.2	2913
0.2-0.3	157
0.3-0.4	13
0.4-0.5	2
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
0.5455	Remote Similarity	NPD3728	Approved

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