NPASS Compound

Natural Product: NPC30841

Natural Product ID	NPC30841
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	OQTHMXQOIPMBIV-JZRZCPCXSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	5318409
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

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 76 81 0 0 0 0 0 0 0 0999 V2000 2.9283 0.3001 -2.2598 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8686 -0.4923 -1.0345 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6675 -0.4828 -0.2010 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7949 0.8346 0.5387 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8704 1.7211 -0.2227 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1282 0.8462 -0.9242 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5345 1.0989 -0.5071 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6873 1.5515 0.9194 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9154 1.0573 1.5943 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1244 0.9856 0.6499 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.2644 0.4885 1.4890 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6509 -0.9329 1.2636 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9901 -1.0044 -0.2341 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.6711 -0.9284 -0.9230 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8682 0.3030 -0.6176 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1873 1.2746 -1.7754 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4089 -0.0806 -0.8517 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9996 -1.3594 -0.2412 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5547 -1.3752 0.1730 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3330 -0.5772 -0.7987 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2885 -1.3295 -2.1103 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8237 0.0683 -0.5318 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.7952 -1.2047 1.9903 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1207 1.1978 0.4833 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8653 0.1708 -0.0589 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3376 -0.8432 0.9187 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6281 -0.5250 1.5913 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5292 0.3811 0.8263 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3892 -0.3620 -0.1754 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1983 -1.2982 0.4458 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7193 1.4277 0.0907 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8977 0.7411 -0.8059 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0552 0.3890 -2.8832 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7366 -0.1403 -2.9215 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3025 1.3552 -2.0914 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2561 -1.5352 -1.1781 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8148 -1.2716 0.5987 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5292 0.7200 1.6165 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3705 2.4743 0.4544 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4574 2.3641 -0.9384 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0620 1.1003 -2.0233 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9450 1.9490 -1.1347 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6476 2.6812 0.9731 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8134 1.2390 1.5631 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1938 1.8318 2.3732 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7934 0.1306 2.1802 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3637 2.0827 0.4735 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2004 1.1036 1.3349 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0658 0.5990 2.5958 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8403 -1.6535 1.4737 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4470 -1.9705 -0.4504 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1210 -1.8748 -0.6814 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8814 -1.0258 -2.0303 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1433 2.3175 -1.4020 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2397 1.1083 -2.1284 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5439 1.0866 -2.6423 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3103 -0.2052 -1.9722 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1302 -2.2122 -0.9741 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5899 -1.6869 0.6442 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1564 -2.4310 0.0866 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3781 -1.0908 1.2159 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0765 -0.7016 -2.9531 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2804 -1.8133 -2.3475 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4226 -2.2022 -2.0869 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7519 -0.2977 -0.6225 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7656 -2.1307 2.3376 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4617 -1.8165 0.3594 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5367 -0.9967 1.6811 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3989 -0.0586 2.5751 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1752 -1.4734 1.7960 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2096 0.8942 1.5405 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7316 -0.8864 -0.9081 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9856 0.3590 -0.7674 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2987 -2.0757 -0.1681 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3733 2.1519 -0.4246 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0763 1.9610 0.8366 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 15 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 13 22 1 0 12 23 1 0 4 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 25 2 1 0 20 3 1 0 32 25 1 0 20 6 1 0 17 7 1 0 15 10 1 0 1 33 1 0 1 34 1 0 1 35 1 0 2 36 1 0 3 37 1 0 4 38 1 0 5 39 1 0 5 40 1 0 6 41 1 0 7 42 1 0 8 43 1 0 8 44 1 0 9 45 1 0 9 46 1 0 10 47 1 6 11 48 1 0 11 49 1 0 12 50 1 0 13 51 1 1 14 52 1 0 14 53 1 0 16 54 1 0 16 55 1 0 16 56 1 0 17 57 1 0 18 58 1 0 18 59 1 0 19 60 1 0 19 61 1 0 21 62 1 0 21 63 1 0 21 64 1 0 22 65 1 0 23 66 1 0 26 67 1 0 26 68 1 0 27 69 1 0 27 70 1 0 28 71 1 0 29 72 1 0 29 73 1 0 30 74 1 0 31 75 1 0 31 76 1 0 M END

Standard InCHIKey	OQTHMXQOIPMBIV-JZRZCPCXSA-N
Standard InCHI	InChI=1S/C27H44O5/c1-15-24-23(32-27(15)9-6-16(13-28)14-31-27)11-20-18-5-4-17-10-21(29)22(30)12-26(17,3)19(18)7-8-25(20,24)2/h15-24,28-30H,4-14H2,1-3H3/t15?,16?,17-,18?,19?,20?,21?,22+,23?,24?,25?,26?,27?/m1/s1
SMILES	CC1C2C(CC3C4CC[C@@H]5CC([C@H](CC5(C)C4CCC23C)O)O)OC21CCC(CO)CO2

Calculated Properties

Physi-Chem Properties

Molecular Weight:	448.32	Volume:	468.16 ? Van der Waals volume.
Dense:	0.958	LogP:	3.034 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.508 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.63 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	1.0	Rigid Bonds:	30.0
TPSA:	79.15 ? Topological Polar Surface Area.	H-Bond Acceptor:	5.0
H-Bond Donor:	3.0	Rings:	6.0
Heavy Atoms:	5.0

MedChem Properties

QED Drug-Likeness Score:	0.57	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.466	Fsp³:	1.0
MCE-18:	142.519 ? 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:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.087	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.083 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.004 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.113	Promiscuous compounds:	0.01

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.107	MDCK Permeability:	-4.864
Pgp-inhibitor:	0.018	Pgp-substrate:	0.151
PAMPA:	0.486 ? 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):	0.004
20% Bioavailability (F20%):	0.088	30% Bioavailability (F30%):	0.12
50% Bioavailability (F50%):	0.757

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.787	MRP1:	0.994
Plasma Protein Binding (PPB):	57.84%	Volume Distribution (VD):	-0.019
Fu:	40.263% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.052
OATP1B3 inhibitor:	0.361	BCRP inhibitor:	0.014
BSEP inhibitor:	0.844

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.012	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.069	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.39	CYP2D6-substrate:	0.004
CYP3A4-inhibitor:	0.004	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.1
HLM stability:	0.097 ? 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):

16.477

Half-life (T1/2):

1.998

ADMET: Toxicity

hERG Blockers:	0.25	hERG Blockers (10um):	0.598
Human Hepatotoxicity (H-HT):	0.581	Drug-induced Liver Injury (DILI):	0.159
AMES Toxicity:	0.166	Rat Oral Acute Toxicity:	0.135
Maximum Recommended Daily Dose:	0.685	Skin Sensitization:	0.173
Carcinogencity:	0.434	Eye Corrosion:	0.0
Eye Irritation:	0.025	Respiratory Toxicity:	0.277
Drug-induced Neurotoxicity:	0.176	Ototoxicity:	0.973
Hematotoxicity:	0.039	Drug-induced Nephrotoxicity:	0.056
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.053
A549 Cytotoxicity:	0.095	Hek293 Cytotoxicity:	0.362
BCF:	1.818 ? 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:	4.072 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.513 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.744 ? 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
NPO22077	Dioscorea tokoro	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO22077	Dioscorea tokoro	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22077	Dioscorea tokoro	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22077	Dioscorea tokoro	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO22077	Dioscorea tokoro	Species	Dioscoreaceae	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 NPC30841 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	24883
0.1-0.2	23550
0.2-0.3	1205
0.3-0.4	132
0.4-0.5	66
0.5-0.6	14
0.6-0.7	5
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8772	High Similarity	NPC227260
0.6875	Remote Similarity	NPC273290
0.6875	Remote Similarity	NPC232044
0.6719	Remote Similarity	NPC248944
0.6719	Remote Similarity	NPC7479
0.6719	Remote Similarity	NPC257296
0.5857	Remote Similarity	NPC481427
0.5676	Remote Similarity	NPC486119
0.5652	Remote Similarity	NPC296734
0.5588	Remote Similarity	NPC24556
0.5417	Remote Similarity	NPC305808
0.5244	Remote Similarity	NPC24960
0.52	Remote Similarity	NPC161035
0.52	Remote Similarity	NPC170438
0.5122	Remote Similarity	NPC473774
0.5122	Remote Similarity	NPC481418
0.5122	Remote Similarity	NPC481419
0.5122	Remote Similarity	NPC481417
0.5116	Remote Similarity	NPC294686
0.5114	Remote Similarity	NPC121453

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC30841 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7255
0.1-0.2	1821
0.2-0.3	66
0.3-0.4	4
0.4-0.5	2
0.5-0.6	0
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
0.6719	Remote Similarity	NPD6928	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