NPASS Compound

Natural Product: NPC575030

Natural Product ID	NPC575030
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	(9~{Z},11~{R},12~{Z})-11-hydroxyoctadeca-9,12-dienoic acid
IUPAC Name	(9~{Z},11~{R},12~{Z})-11-hydroxyoctadeca-9,12-dienoic acid
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 53 52 0 0 0 0 0 0 0 0999 V2000 6.6700 0.6087 -1.5948 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4187 -0.5218 -0.6394 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7173 -0.0754 0.6166 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3773 0.5449 0.3504 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4632 -0.4106 -0.3403 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2603 -1.6028 0.5004 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0437 -1.9086 0.9055 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9150 -1.0515 0.5087 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.2835 -1.6702 0.9490 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9384 0.2780 1.1396 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2838 1.2872 0.6053 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5250 1.2636 -0.6219 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9672 1.6765 -0.3238 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5372 0.7090 0.6495 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9643 1.0227 1.0433 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9122 1.0279 -0.0906 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0493 -0.2272 -0.8544 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4992 -1.4243 -0.1273 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8417 -1.2810 0.4844 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3525 -2.2194 1.1880 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6470 -0.1600 0.3598 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7293 1.0799 -1.9583 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3144 1.3499 -1.0450 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1967 0.2013 -2.4723 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4377 -0.8792 -0.3098 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9219 -1.3918 -1.0652 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5950 -0.9578 1.2706 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3922 0.6098 1.1781 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4531 1.5246 -0.1670 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9427 0.7880 1.3645 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0087 -0.7268 -1.2852 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5371 0.0500 -0.7149 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1087 -2.2178 0.7743 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8899 -2.7844 1.5243 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8256 -1.0080 -0.5804 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0922 -2.4403 1.5288 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4940 0.4571 2.0574 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3449 2.2481 1.1257 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1654 2.0448 -1.3576 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5662 0.3117 -1.1522 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9034 2.7086 0.0855 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4859 1.6495 -1.3151 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4821 -0.3046 0.1470 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8621 0.6335 1.5206 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2619 0.3852 1.9007 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9351 2.0679 1.4612 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5880 1.8720 -0.7745 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9160 1.3596 0.2448 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7114 -0.0994 -1.7521 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0391 -0.4544 -1.3102 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8064 -1.7958 0.6521 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5955 -2.2917 -0.8475 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2900 0.1449 1.1033 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 2 0 7 8 1 0 8 9 1 0 8 10 1 0 10 11 2 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 2 0 19 21 1 0 1 22 1 0 1 23 1 0 1 24 1 0 2 25 1 0 2 26 1 0 3 27 1 0 3 28 1 0 4 29 1 0 4 30 1 0 5 31 1 0 5 32 1 0 6 33 1 0 7 34 1 0 8 35 1 6 9 36 1 0 10 37 1 0 11 38 1 0 12 39 1 0 12 40 1 0 13 41 1 0 13 42 1 0 14 43 1 0 14 44 1 0 15 45 1 0 15 46 1 0 16 47 1 0 16 48 1 0 17 49 1 0 17 50 1 0 18 51 1 0 18 52 1 0 21 53 1 0 M END

Standard InCHIKey	GIJZWHLTBMCTJV-LILDEJAOSA-N
Standard InCHI	InChI=1S/C18H32O3/c1-2-3-4-8-11-14-17(19)15-12-9-6-5-7-10-13-16-18(20)21/h11-12,14-15,17,19H,2-10,13,16H2,1H3,(H,20,21)/b14-11-,15-12-/t17-/m1/s1
SMILES	CCCCC/C=C[C@@H](O)/C=CCCCCCCCC(=O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	296.24	Volume:	338.345 ? Van der Waals volume.
Dense:	0.876	LogP:	4.649 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.1 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.713 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	14.0	Rigid Bonds:	3.0
TPSA:	57.53 ? Topological Polar Surface Area.	H-Bond Acceptor:	3.0
H-Bond Donor:	2.0	Rings:	0.0
Heavy Atoms:	3.0

MedChem Properties

QED Drug-Likeness Score:	0.355	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.025	Fsp³:	0.722
MCE-18:	2.0 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.107	Fluc inhibitor:	0.004 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.003 ? 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:	0.986	Promiscuous compounds:	0.849

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.034	MDCK Permeability:	-4.781
Pgp-inhibitor:	0.001	Pgp-substrate:	0.001
PAMPA:	0.159 ? 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):	0.028
20% Bioavailability (F20%):	0.174	30% Bioavailability (F30%):	0.869
50% Bioavailability (F50%):	0.614

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.937
Plasma Protein Binding (PPB):	91.983%	Volume Distribution (VD):	-0.025
Fu:	5.618% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.01
OATP1B3 inhibitor:	0.713	BCRP inhibitor:	0.019
BSEP inhibitor:	0.99

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.002
CYP2C19-inhibitor:	0.004	CYP2C19-substrate:	0.958
CYP2C9-inhibitor:	0.996	CYP2C9-substrate:	0.042
CYP2D6-inhibitor:	0.083	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.865
CYP2B6-substrate:	0.443	CYP2C8-inhibitor:	0.994
HLM stability:	0.044 ? 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):

3.648

Half-life (T1/2):

0.778

ADMET: Toxicity

hERG Blockers:	0.068	hERG Blockers (10um):	0.155
Human Hepatotoxicity (H-HT):	0.228	Drug-induced Liver Injury (DILI):	0.001
AMES Toxicity:	0.083	Rat Oral Acute Toxicity:	0.007
Maximum Recommended Daily Dose:	0.019	Skin Sensitization:	1.0
Carcinogencity:	0.006	Eye Corrosion:	0.994
Eye Irritation:	1.0	Respiratory Toxicity:	0.852
Drug-induced Neurotoxicity:	0.003	Ototoxicity:	0.364
Hematotoxicity:	0.007	Drug-induced Nephrotoxicity:	0.405
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.047
A549 Cytotoxicity:	0.052	Hek293 Cytotoxicity:	0.015
BCF:	1.131 ? 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:	4.001 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.315 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	2.9 ? 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
NPO8339	Lithothamnion corallioides	Species	Hapalidiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8339	Lithothamnion corallioides	Species	Hapalidiaceae	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 NPC575030 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	27210
0.1-0.2	20154
0.2-0.3	2010
0.3-0.4	292
0.4-0.5	101
0.5-0.6	42
0.6-0.7	26
0.7-0.8	2
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
0.7353	Intermediate Similarity	NPC424
0.7353	Intermediate Similarity	NPC36061
0.7353	Intermediate Similarity	NPC69510
0.7353	Intermediate Similarity	NPC77272
0.7353	Intermediate Similarity	NPC290563
0.7353	Intermediate Similarity	NPC139029
0.7353	Intermediate Similarity	NPC281972
0.7353	Intermediate Similarity	NPC261831
0.7353	Intermediate Similarity	NPC87564
0.7143	Intermediate Similarity	NPC95145
0.7143	Intermediate Similarity	NPC325642
0.7143	Intermediate Similarity	NPC65174
0.7073	Intermediate Similarity	NPC255863
0.7073	Intermediate Similarity	NPC136164
0.7073	Intermediate Similarity	NPC245947
0.7059	Intermediate Similarity	NPC281245
0.6857	Remote Similarity	NPC92114
0.6757	Remote Similarity	NPC154245
0.6757	Remote Similarity	NPC85813
0.6757	Remote Similarity	NPC223697
0.6757	Remote Similarity	NPC6095
0.6667	Remote Similarity	NPC243532
0.65	Remote Similarity	NPC606120
0.6486	Remote Similarity	NPC321062
0.6061	Remote Similarity	NPC171736
0.6061	Remote Similarity	NPC301585
0.6061	Remote Similarity	NPC261080
0.6061	Remote Similarity	NPC132565
0.6061	Remote Similarity	NPC209970
0.6061	Remote Similarity	NPC216630
0.6061	Remote Similarity	NPC201844
0.6061	Remote Similarity	NPC301696
0.6061	Remote Similarity	NPC196924
0.6061	Remote Similarity	NPC307783
0.6061	Remote Similarity	NPC154186
0.6061	Remote Similarity	NPC149184
0.6061	Remote Similarity	NPC279026
0.6061	Remote Similarity	NPC113928
0.6061	Remote Similarity	NPC14227
0.6053	Remote Similarity	NPC5413
0.6053	Remote Similarity	NPC324004
0.6053	Remote Similarity	NPC328497
0.5909	Remote Similarity	NPC99619
0.5897	Remote Similarity	NPC52955
0.5897	Remote Similarity	NPC88966
0.5897	Remote Similarity	NPC25417
0.5897	Remote Similarity	NPC1813
0.5897	Remote Similarity	NPC59051
0.587	Remote Similarity	NPC323045
0.587	Remote Similarity	NPC49863
0.587	Remote Similarity	NPC317881
0.5814	Remote Similarity	NPC106851
0.5814	Remote Similarity	NPC282788
0.5814	Remote Similarity	NPC274927
0.5814	Remote Similarity	NPC477201
0.5778	Remote Similarity	NPC318420
0.5778	Remote Similarity	NPC326268
0.5758	Remote Similarity	NPC155263
0.5682	Remote Similarity	NPC179764
0.5652	Remote Similarity	NPC470320
0.5641	Remote Similarity	NPC91495
0.5641	Remote Similarity	NPC70387
0.5625	Remote Similarity	NPC605544
0.5625	Remote Similarity	NPC607260
0.5556	Remote Similarity	NPC180534
0.5556	Remote Similarity	NPC251042
0.5556	Remote Similarity	NPC174447
0.5556	Remote Similarity	NPC122521
0.5556	Remote Similarity	NPC611531
0.5435	Remote Similarity	NPC68343
0.5435	Remote Similarity	NPC328089
0.5349	Remote Similarity	NPC487561
0.5349	Remote Similarity	NPC225929
0.5319	Remote Similarity	NPC327112
0.5263	Remote Similarity	NPC34416
0.5217	Remote Similarity	NPC473863
0.5208	Remote Similarity	NPC26500
0.5152	Remote Similarity	NPC214610
0.5152	Remote Similarity	NPC118968
0.5152	Remote Similarity	NPC183424
0.5152	Remote Similarity	NPC294085
0.5128	Remote Similarity	NPC8219
0.5106	Remote Similarity	NPC325627
0.5106	Remote Similarity	NPC323477

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC575030 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6002
0.1-0.2	2842
0.2-0.3	251
0.3-0.4	27
0.4-0.5	13
0.5-0.6	6
0.6-0.7	6
0.7-0.8	2
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
0.7353	Intermediate Similarity	NPD3195	Phase 2
0.7353	Intermediate Similarity	NPD3196	Approved
0.6923	Remote Similarity	NPD3194	Phase 4
0.6757	Remote Similarity	NPD4266	Phase 2
0.6061	Remote Similarity	NPD2270	Pre-clinical
0.6061	Remote Similarity	NPD633	Phase 3
0.6061	Remote Similarity	NPD9448	Phase 2
0.6053	Remote Similarity	NPD3173	Phase 4
0.5897	Remote Similarity	NPD3172	Approved
0.587	Remote Similarity	NPD4247	Clinical (unspecified phase)
0.5556	Remote Similarity	NPD622	Pre-clinical
0.5435	Remote Similarity	NPD39	Phase 4
0.5319	Remote Similarity	NPD4246	Phase 2
0.5152	Remote Similarity	NPD9655	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