NPASS Compound

Natural Product: NPC9805

Natural Product ID	NPC9805
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	AKVZFALHMAASOY-XAEZVHHGSA-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] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0000262] Fatty acids and conjugates [CHEMONTID:0002950] Very long-chain fatty acids

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 74 73 0 0 0 0 0 0 0 0999 V2000 -11.7484 -0.1166 -0.9911 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.3797 0.2545 0.4110 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.9424 0.7534 0.4685 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.9979 -0.3140 -0.0056 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5610 0.1641 0.0357 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0914 0.5462 1.4019 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6667 1.0154 1.3376 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7747 -0.0599 0.8216 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3097 0.4179 0.7779 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5002 -0.7317 0.2482 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0156 -0.3688 0.1673 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3215 -1.5925 -0.3723 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1506 -1.4700 -0.5277 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6405 -0.4022 -1.4417 C 0 0 2 0 0 0 0 0 0 0 0 0 3.1485 -0.4909 -1.4292 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8684 0.0950 -0.4878 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3941 0.0030 -0.4784 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8194 -0.6437 0.7858 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2521 -0.8787 1.0169 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2178 0.2158 1.1093 C 0 0 0 0 0 0 0 0 0 0 0 0 8.4457 1.1245 -0.0373 C 0 0 0 0 0 0 0 0 0 0 0 0 8.8863 0.4056 -1.2778 C 0 0 0 0 0 0 0 0 0 0 0 0 10.1550 -0.3465 -1.1080 C 0 0 0 0 0 0 0 0 0 0 0 0 11.3432 0.4370 -0.7706 C 0 0 0 0 0 0 0 0 0 0 0 0 11.4191 1.6763 -0.6596 O 0 0 0 0 0 0 0 0 0 0 0 0 12.5472 -0.2564 -0.5409 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2166 0.8717 -1.1452 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5413 -2.6071 0.5898 O 0 0 0 0 0 0 0 0 0 0 0 0 -12.8485 0.0103 -1.1067 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.5512 -1.1969 -1.2138 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.2019 0.4966 -1.7135 H 0 0 0 0 0 0 0 0 0 0 0 0 -12.0558 1.0573 0.7622 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.4360 -0.6310 1.0702 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.8633 1.6002 -0.2649 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.6964 1.1612 1.4583 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.0298 -1.2213 0.6614 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.2664 -0.5891 -1.0421 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9370 -0.6737 -0.3908 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4656 0.9892 -0.6936 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1073 -0.3854 2.0423 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7543 1.3064 1.8850 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2951 1.3783 2.3182 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6286 1.8802 0.6269 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9868 -0.3608 -0.2321 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8028 -0.9644 1.4621 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9734 0.7246 1.7814 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2466 1.2447 0.0311 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6755 -1.6254 0.8703 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8242 -0.9336 -0.7953 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6552 -0.1687 1.1772 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9670 0.5106 -0.5161 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8011 -1.9588 -1.3137 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5479 -2.4582 -0.8879 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6051 -1.3023 0.4906 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3087 -0.6351 -2.4897 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6721 -1.0412 -2.1983 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3572 0.6512 0.2907 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6520 -0.7019 -1.3176 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7107 1.0197 -0.6664 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3182 -0.1381 1.6771 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3208 -1.6723 0.8234 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4078 -1.5237 1.9542 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5940 -1.6176 0.2132 H 0 0 0 0 0 0 0 0 0 0 0 0 9.2320 -0.2607 1.3345 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0533 0.8519 2.0256 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6998 1.8912 -0.2374 H 0 0 0 0 0 0 0 0 0 0 0 0 9.3668 1.7561 0.2535 H 0 0 0 0 0 0 0 0 0 0 0 0 8.9949 1.2005 -2.0711 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0406 -0.2645 -1.5906 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3691 -0.9015 -2.0734 H 0 0 0 0 0 0 0 0 0 0 0 0 9.9542 -1.1485 -0.3413 H 0 0 0 0 0 0 0 0 0 0 0 0 13.2456 0.1010 0.1136 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8699 1.5761 -1.3934 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0953 -2.3849 1.3287 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 2 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 24 25 2 0 24 26 1 0 14 27 1 0 12 28 1 0 1 29 1 0 1 30 1 0 1 31 1 0 2 32 1 0 2 33 1 0 3 34 1 0 3 35 1 0 4 36 1 0 4 37 1 0 5 38 1 0 5 39 1 0 6 40 1 0 6 41 1 0 7 42 1 0 7 43 1 0 8 44 1 0 8 45 1 0 9 46 1 0 9 47 1 0 10 48 1 0 10 49 1 0 11 50 1 0 11 51 1 0 12 52 1 6 13 53 1 0 13 54 1 0 14 55 1 6 15 56 1 0 16 57 1 0 17 58 1 0 17 59 1 0 18 60 1 0 18 61 1 0 19 62 1 0 19 63 1 0 20 64 1 0 20 65 1 0 21 66 1 0 21 67 1 0 22 68 1 0 22 69 1 0 23 70 1 0 23 71 1 0 26 72 1 0 27 73 1 0 28 74 1 0 M END

Standard InCHIKey	AKVZFALHMAASOY-XAEZVHHGSA-N
Standard InCHI	InChI=1S/C24H46O4/c1-2-3-4-5-6-7-9-12-15-18-22(25)21-23(26)19-16-13-10-8-11-14-17-20-24(27)28/h16,19,22-23,25-26H,2-15,17-18,20-21H2,1H3,(H,27,28)/b19-16+/t22-,23-/m0/s1
SMILES	CCCCCCCCCCC[C@@H](C[C@H](/C=C/CCCCCCCC(=O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	398.34	Volume:	453.548 ? Van der Waals volume.
Dense:	0.878	LogP:	5.694 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.483 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.902 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	21.0	Rigid Bonds:	2.0
TPSA:	77.76 ? Topological Polar Surface Area.	H-Bond Acceptor:	4.0
H-Bond Donor:	3.0	Rings:	0.0
Heavy Atoms:	4.0

MedChem Properties

QED Drug-Likeness Score:	0.155	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.122	Fsp³:	0.875
MCE-18:	3.0 ? 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:	0.494	Fluc inhibitor:	0.004 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.002 ? 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:	0.932	Promiscuous compounds:	0.551

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.243	MDCK Permeability:	-4.797
Pgp-inhibitor:	0.0	Pgp-substrate:	0.044
PAMPA:	0.386 ? 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):	0.612
20% Bioavailability (F20%):	0.964	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	0.985

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.435
Plasma Protein Binding (PPB):	97.205%	Volume Distribution (VD):	0.338
Fu:	2.202% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.514
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.195
BSEP inhibitor:	0.792

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.002
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.003
CYP2C9-inhibitor:	0.986	CYP2C9-substrate:	0.359
CYP2D6-inhibitor:	0.997	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.01 ? 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):

4.135

Half-life (T1/2):

1.114

ADMET: Toxicity

hERG Blockers:	0.107	hERG Blockers (10um):	0.326
Human Hepatotoxicity (H-HT):	0.712	Drug-induced Liver Injury (DILI):	0.07
AMES Toxicity:	0.009	Rat Oral Acute Toxicity:	0.044
Maximum Recommended Daily Dose:	0.721	Skin Sensitization:	0.987
Carcinogencity:	0.205	Eye Corrosion:	0.632
Eye Irritation:	0.988	Respiratory Toxicity:	0.982
Drug-induced Neurotoxicity:	0.042	Ototoxicity:	0.661
Hematotoxicity:	0.188	Drug-induced Nephrotoxicity:	0.752
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.052
A549 Cytotoxicity:	0.431	Hek293 Cytotoxicity:	0.068
BCF:	0.873 ? 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:	4.241 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.74 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	2.128 ? 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
NPO1454	Spondias mombin	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8064298]
NPO1454	Spondias mombin	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1454	Spondias mombin	Species	Anacardiaceae	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 NPC9805 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	28262
0.1-0.2	19363
0.2-0.3	1838
0.3-0.4	241
0.4-0.5	87
0.5-0.6	23
0.6-0.7	13
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
0.7111	Intermediate Similarity	NPC243532
0.7111	Intermediate Similarity	NPC255863
0.7111	Intermediate Similarity	NPC136164
0.7111	Intermediate Similarity	NPC245947
0.6977	Remote Similarity	NPC606120
0.6585	Remote Similarity	NPC324004
0.6585	Remote Similarity	NPC328497
0.6098	Remote Similarity	NPC424
0.6098	Remote Similarity	NPC36061
0.6098	Remote Similarity	NPC69510
0.6098	Remote Similarity	NPC77272
0.6098	Remote Similarity	NPC290563
0.6098	Remote Similarity	NPC139029
0.6098	Remote Similarity	NPC281972
0.6098	Remote Similarity	NPC261831
0.6098	Remote Similarity	NPC87564
0.6042	Remote Similarity	NPC99619
0.5952	Remote Similarity	NPC95145
0.5952	Remote Similarity	NPC325642
0.5952	Remote Similarity	NPC65174
0.5854	Remote Similarity	NPC281245
0.58	Remote Similarity	NPC470320
0.5714	Remote Similarity	NPC92114
0.5686	Remote Similarity	NPC323045
0.5686	Remote Similarity	NPC49863
0.5686	Remote Similarity	NPC317881
0.5682	Remote Similarity	NPC154245
0.5682	Remote Similarity	NPC85813
0.5682	Remote Similarity	NPC223697
0.5682	Remote Similarity	NPC6095
0.549	Remote Similarity	NPC327112
0.5455	Remote Similarity	NPC88735
0.5455	Remote Similarity	NPC321062
0.5385	Remote Similarity	NPC26500
0.5306	Remote Similarity	NPC477201
0.5294	Remote Similarity	NPC325627
0.5185	Remote Similarity	NPC605544
0.5185	Remote Similarity	NPC607260
0.5172	Remote Similarity	NPC47031
0.5111	Remote Similarity	NPC5413

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC9805 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6398
0.1-0.2	2516
0.2-0.3	192
0.3-0.4	19
0.4-0.5	14
0.5-0.6	5
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	Drug ID	Developmental Stage
0.6098	Remote Similarity	NPD3195	Phase 2
0.6098	Remote Similarity	NPD3196	Approved
0.587	Remote Similarity	NPD3194	Phase 4
0.5686	Remote Similarity	NPD4247	Clinical (unspecified phase)
0.5682	Remote Similarity	NPD4266	Phase 2
0.549	Remote Similarity	NPD4246	Phase 2
0.5111	Remote Similarity	NPD3173	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