NPASS Compound

Natural Product: NPC311622

Natural Product ID	NPC311622
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	BWDBEAQIHAEVLV-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	15450
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0001334] Fatty alcohols

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 27 26 0 0 0 0 0 0 0 0999 V2000 -1.7237 -1.5492 0.4494 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9570 -0.3840 -0.4874 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9500 0.5303 0.1372 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6514 0.2730 -0.8332 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0813 0.8082 0.3587 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3822 1.4596 -0.0322 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3631 0.5826 -0.7174 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8389 -0.6088 0.0373 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8393 -1.4842 0.3839 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6008 -2.2587 0.4363 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6417 -1.2221 1.5169 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8267 -2.1279 0.1820 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3989 -0.8041 -1.4138 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7478 0.5819 1.2220 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9595 0.0776 0.0219 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0095 1.5339 -0.3342 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8314 1.1251 -1.5201 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0021 -0.4479 -1.3551 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2913 0.0506 1.1403 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5222 1.5906 0.9027 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1002 2.2560 -0.7854 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8233 2.0239 0.8210 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2378 1.2117 -1.0554 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8894 0.2034 -1.6681 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5343 -1.1648 -0.6568 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4528 -0.3492 0.9302 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9887 -1.9076 1.2527 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 1 10 1 0 1 11 1 0 1 12 1 0 2 13 1 0 3 14 1 0 3 15 1 0 3 16 1 0 4 17 1 0 4 18 1 0 5 19 1 0 5 20 1 0 6 21 1 0 6 22 1 0 7 23 1 0 7 24 1 0 8 25 1 0 8 26 1 0 9 27 1 0 M END

Standard InCHIKey	BWDBEAQIHAEVLV-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C8H18O/c1-8(2)6-4-3-5-7-9/h8-9H,3-7H2,1-2H3
SMILES	CC(C)CCCCCO

Calculated Properties

Physi-Chem Properties

Molecular Weight:	130.14	Volume:	155.715 ? Van der Waals volume.
Dense:	0.836	LogP:	2.694 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.394 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.1 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	5.0	Rigid Bonds:	0.0
TPSA:	20.23 ? Topological Polar Surface Area.	H-Bond Acceptor:	1.0
H-Bond Donor:	1.0	Rings:	0.0
Heavy Atoms:	1.0

MedChem Properties

QED Drug-Likeness Score:	0.566	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	1.756	Fsp³:	1.0
MCE-18:	0.0 ? 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:	Accepted	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.005	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.001 ? 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:	0.999	Promiscuous compounds:	0.222

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.04	MDCK Permeability:	-4.738
Pgp-inhibitor:	0.091	Pgp-substrate:	0.075
PAMPA:	0.192 ? 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):	0.056
20% Bioavailability (F20%):	0.025	30% Bioavailability (F30%):	0.213
50% Bioavailability (F50%):	0.285

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.941	MRP1:	0.723
Plasma Protein Binding (PPB):	54.246%	Volume Distribution (VD):	0.018
Fu:	48.212% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.06
OATP1B3 inhibitor:	0.223	BCRP inhibitor:	0.318
BSEP inhibitor:	0.06

ADMET: Metabolism

CYP1A2-inhibitor:	0.15	CYP1A2-substrate:	0.704
CYP2C19-inhibitor:	0.936	CYP2C19-substrate:	0.508
CYP2C9-inhibitor:	0.8	CYP2C9-substrate:	0.032
CYP2D6-inhibitor:	0.779	CYP2D6-substrate:	0.738
CYP3A4-inhibitor:	0.146	CYP3A4-substrate:	0.568
CYP2B6-substrate:	0.133	CYP2C8-inhibitor:	0.975
HLM stability:	0.994 ? 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):

9.233

Half-life (T1/2):

0.894

ADMET: Toxicity

hERG Blockers:	0.122	hERG Blockers (10um):	0.499
Human Hepatotoxicity (H-HT):	0.522	Drug-induced Liver Injury (DILI):	0.079
AMES Toxicity:	0.276	Rat Oral Acute Toxicity:	0.136
Maximum Recommended Daily Dose:	0.091	Skin Sensitization:	0.833
Carcinogencity:	0.495	Eye Corrosion:	0.988
Eye Irritation:	0.998	Respiratory Toxicity:	0.604
Drug-induced Neurotoxicity:	0.123	Ototoxicity:	0.341
Hematotoxicity:	0.255	Drug-induced Nephrotoxicity:	0.246
Genotoxicity:	0.002	RPMI-8226 Immunitoxicity:	0.043
A549 Cytotoxicity:	0.067	Hek293 Cytotoxicity:	0.049
BCF:	1.522 ? 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:	3.319 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.302 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.782 ? 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
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	cone	n.a.	PMID[10336650]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	leaf	n.a.	PMID[15388977]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15679315]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16252923]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	stem	n.a.	PMID[17202689]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	cone	n.a.	PMID[17624889]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18611049]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18768384]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19476340]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	pericarp	n.a.	PMID[20628994]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21912858]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	cone	n.a.	PMID[22111577]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	flower	n.a.	PMID[22166201]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23790907]
NPO5315	Zanthoxylum bungeanum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24175626]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24948953]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25564559]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29154541]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30384263]
NPO8698	Zanthoxylum schinifolium	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[35537359]
NPO5315	Zanthoxylum bungeanum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[36786362]
NPO8698	Zanthoxylum schinifolium	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37029634]
NPO5315	Zanthoxylum bungeanum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37029634]
NPO5315	Zanthoxylum bungeanum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37049761]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37631012]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38354824]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[39199155]
NPO8698	Zanthoxylum schinifolium	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO5315	Zanthoxylum bungeanum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO5315	Zanthoxylum bungeanum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8698	Zanthoxylum schinifolium	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5315	Zanthoxylum bungeanum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8698	Zanthoxylum schinifolium	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8698	Zanthoxylum schinifolium	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5315	Zanthoxylum bungeanum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8698	Zanthoxylum schinifolium	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO5315	Zanthoxylum bungeanum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8698	Zanthoxylum schinifolium	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5315	Zanthoxylum bungeanum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13879	Humulus lupulus	Species	Cannabaceae	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 NPC311622 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	33658
0.1-0.2	15536
0.2-0.3	582
0.3-0.4	44
0.4-0.5	13
0.5-0.6	19
0.6-0.7	3
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
0.7368	Intermediate Similarity	NPC469759
0.7368	Intermediate Similarity	NPC160261
0.6471	Remote Similarity	NPC39869
0.625	Remote Similarity	NPC213764
0.6111	Remote Similarity	NPC275462
0.5882	Remote Similarity	NPC152759
0.5882	Remote Similarity	NPC12231
0.5789	Remote Similarity	NPC126915
0.5789	Remote Similarity	NPC205141
0.5789	Remote Similarity	NPC24506
0.5789	Remote Similarity	NPC225783
0.5789	Remote Similarity	NPC279895
0.5789	Remote Similarity	NPC185538
0.5789	Remote Similarity	NPC181516
0.5789	Remote Similarity	NPC163556
0.5789	Remote Similarity	NPC139131
0.5789	Remote Similarity	NPC236797
0.5789	Remote Similarity	NPC291158
0.5789	Remote Similarity	NPC272998
0.5789	Remote Similarity	NPC112242
0.5789	Remote Similarity	NPC185041
0.5789	Remote Similarity	NPC147096
0.5455	Remote Similarity	NPC490059
0.5294	Remote Similarity	NPC256186

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC311622 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7679
0.1-0.2	1419
0.2-0.3	49
0.3-0.4	0
0.4-0.5	1
0.5-0.6	2
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
0.5789	Remote Similarity	NPD2272	Phase 4
0.5789	Remote Similarity	NPD5383	Phase 4

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