NPASS Compound

Natural Product: NPC1504

Natural Product ID	NPC1504
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	NPDSHTNEKLQQIJ-WXUVIADPSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	16061059
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0000504] Lineolic acids and derivatives

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 -6.6503 2.1193 -1.2692 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9951 1.0657 -2.0881 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6204 -0.1824 -1.4337 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5767 -0.2021 -0.3468 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8072 0.5663 0.8520 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9626 0.6396 2.0058 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8342 0.0844 2.2607 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1245 -0.7919 1.3789 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9407 -1.3278 1.7441 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1920 -2.2330 0.8521 C 0 0 1 0 0 0 0 0 0 0 0 0 1.2747 -1.8705 0.9639 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4214 -0.4288 0.5341 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8619 0.0373 0.6102 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7777 -0.7493 -0.2528 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1870 -0.2386 -0.1052 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3520 1.1904 -0.4918 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7446 1.7142 -0.3645 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7502 1.0310 -1.1974 C 0 0 0 0 0 0 0 0 0 0 0 0 8.9473 1.3935 -1.0691 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4690 0.0272 -2.1040 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3112 -3.5696 1.2284 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5169 2.6069 -1.8612 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1597 1.6990 -0.3915 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0243 3.0082 -1.0415 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1575 1.5051 -2.7251 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7532 0.7959 -2.9000 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2943 -0.9728 -2.1909 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5841 -0.6549 -1.0438 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4671 -1.3003 -0.1244 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6384 0.1881 -0.8518 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8502 0.2589 1.2469 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0676 1.6481 0.5191 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3492 1.3152 2.8747 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3442 0.3023 3.2796 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4253 -1.0885 0.4169 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5760 -1.0593 2.7167 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5016 -2.0637 -0.2050 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5467 -2.0077 2.0306 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9210 -2.5521 0.3837 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8542 0.1905 1.2592 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0228 -0.2403 -0.4629 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2496 0.1267 1.6327 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8233 1.0901 0.1985 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8029 -1.8328 -0.0207 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5371 -0.6878 -1.3364 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5346 -0.4177 0.9549 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8439 -0.8674 -0.7439 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0183 1.2874 -1.5572 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6640 1.8293 0.1281 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0855 1.6024 0.6952 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7156 2.8042 -0.6032 H 0 0 0 0 0 0 0 0 0 0 0 0 8.1539 -0.7020 -2.3432 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8343 -4.0859 0.5741 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 2 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 2 0 18 20 1 0 10 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 0 9 36 1 0 10 37 1 6 11 38 1 0 11 39 1 0 12 40 1 0 12 41 1 0 13 42 1 0 13 43 1 0 14 44 1 0 14 45 1 0 15 46 1 0 15 47 1 0 16 48 1 0 16 49 1 0 17 50 1 0 17 51 1 0 20 52 1 0 21 53 1 0 M END

Standard InCHIKey	NPDSHTNEKLQQIJ-WXUVIADPSA-N
Standard InCHI	InChI=1S/C18H32O3/c1-2-3-4-5-6-8-11-14-17(19)15-12-9-7-10-13-16-18(20)21/h6,8,11,14,17,19H,2-5,7,9-10,12-13,15-16H2,1H3,(H,20,21)/b8-6-,14-11+/t17-/m0/s1
SMILES	CCCCC/C=CC=C[C@@H](CCCCCCCC(=O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	296.24	Volume:	338.345 ? Van der Waals volume.
Dense:	0.876	LogP:	4.241 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.083 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.764 ? 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:	2.873	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:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.188	Fluc inhibitor:	0.014 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.006 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.013 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.984	Promiscuous compounds:	0.443

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.165	MDCK Permeability:	-4.785
Pgp-inhibitor:	0.002	Pgp-substrate:	0.252
PAMPA:	0.608 ? 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):	0.398
20% Bioavailability (F20%):	0.68	30% Bioavailability (F30%):	0.977
50% Bioavailability (F50%):	0.848

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.003	MRP1:	0.788
Plasma Protein Binding (PPB):	96.381%	Volume Distribution (VD):	-0.393
Fu:	3.663% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.01
OATP1B3 inhibitor:	0.501	BCRP inhibitor:	0.179
BSEP inhibitor:	0.995

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.014
CYP2C19-inhibitor:	0.001	CYP2C19-substrate:	0.231
CYP2C9-inhibitor:	0.991	CYP2C9-substrate:	0.055
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.992
HLM stability:	0.037 ? 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):

4.256

Half-life (T1/2):

0.893

ADMET: Toxicity

hERG Blockers:	0.127	hERG Blockers (10um):	0.304
Human Hepatotoxicity (H-HT):	0.554	Drug-induced Liver Injury (DILI):	0.032
AMES Toxicity:	0.134	Rat Oral Acute Toxicity:	0.173
Maximum Recommended Daily Dose:	0.597	Skin Sensitization:	0.997
Carcinogencity:	0.196	Eye Corrosion:	0.913
Eye Irritation:	0.988	Respiratory Toxicity:	0.887
Drug-induced Neurotoxicity:	0.047	Ototoxicity:	0.652
Hematotoxicity:	0.216	Drug-induced Nephrotoxicity:	0.554
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.044
A549 Cytotoxicity:	0.222	Hek293 Cytotoxicity:	0.095
BCF:	1.127 ? 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:	3.991 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.274 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.443 ? 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
NPO1004	Consolida scleroclada	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3822	Rhodophiala bifida	Species	Amaryllidaceae	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 NPC1504 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	28103
0.1-0.2	19377
0.2-0.3	1914
0.3-0.4	283
0.4-0.5	89
0.5-0.6	52
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	3

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC255863
1.0	High Similarity	NPC136164
1.0	High Similarity	NPC245947
0.75	Intermediate Similarity	NPC323045
0.75	Intermediate Similarity	NPC317881
0.7297	Intermediate Similarity	NPC95145
0.7297	Intermediate Similarity	NPC325642
0.7297	Intermediate Similarity	NPC65174
0.7273	Intermediate Similarity	NPC327112
0.7111	Intermediate Similarity	NPC49863
0.6818	Remote Similarity	NPC243532
0.6818	Remote Similarity	NPC99619
0.6667	Remote Similarity	NPC325627
0.6667	Remote Similarity	NPC606120
0.6579	Remote Similarity	NPC424
0.6579	Remote Similarity	NPC36061
0.6579	Remote Similarity	NPC69510
0.6579	Remote Similarity	NPC77272
0.6579	Remote Similarity	NPC290563
0.6579	Remote Similarity	NPC139029
0.6579	Remote Similarity	NPC281972
0.6579	Remote Similarity	NPC261831
0.6579	Remote Similarity	NPC87564
0.6522	Remote Similarity	NPC470320
0.6458	Remote Similarity	NPC605544
0.6458	Remote Similarity	NPC607260
0.6316	Remote Similarity	NPC281245
0.6304	Remote Similarity	NPC323477
0.625	Remote Similarity	NPC324004
0.625	Remote Similarity	NPC328497
0.6154	Remote Similarity	NPC92114
0.6098	Remote Similarity	NPC154245
0.6098	Remote Similarity	NPC85813
0.6098	Remote Similarity	NPC223697
0.6098	Remote Similarity	NPC6095
0.6042	Remote Similarity	NPC26500
0.5957	Remote Similarity	NPC318420
0.5957	Remote Similarity	NPC326268
0.587	Remote Similarity	NPC324475
0.5854	Remote Similarity	NPC321062
0.5814	Remote Similarity	NPC318306
0.58	Remote Similarity	NPC328653
0.5769	Remote Similarity	NPC88735
0.5745	Remote Similarity	NPC251042
0.5745	Remote Similarity	NPC174447
0.5745	Remote Similarity	NPC122521
0.5556	Remote Similarity	NPC192006
0.5556	Remote Similarity	NPC227396
0.5476	Remote Similarity	NPC5413
0.5455	Remote Similarity	NPC7414
0.5455	Remote Similarity	NPC279537
0.5455	Remote Similarity	NPC47031
0.5405	Remote Similarity	NPC171736
0.5405	Remote Similarity	NPC301585
0.5405	Remote Similarity	NPC261080
0.5405	Remote Similarity	NPC132565
0.5405	Remote Similarity	NPC209970
0.5405	Remote Similarity	NPC216630
0.5405	Remote Similarity	NPC201844
0.5405	Remote Similarity	NPC301696
0.5405	Remote Similarity	NPC196924
0.5405	Remote Similarity	NPC307783
0.5405	Remote Similarity	NPC154186
0.5405	Remote Similarity	NPC149184
0.5405	Remote Similarity	NPC279026
0.5405	Remote Similarity	NPC113928
0.5405	Remote Similarity	NPC14227
0.537	Remote Similarity	NPC260814
0.537	Remote Similarity	NPC323249
0.537	Remote Similarity	NPC27949
0.537	Remote Similarity	NPC39547
0.5349	Remote Similarity	NPC52955
0.5349	Remote Similarity	NPC88966
0.5349	Remote Similarity	NPC25417
0.5349	Remote Similarity	NPC1813
0.5349	Remote Similarity	NPC472808
0.5349	Remote Similarity	NPC59051
0.5319	Remote Similarity	NPC106851
0.5319	Remote Similarity	NPC282788
0.5319	Remote Similarity	NPC274927
0.5319	Remote Similarity	NPC477201
0.5263	Remote Similarity	NPC316844
0.5217	Remote Similarity	NPC225929
0.5208	Remote Similarity	NPC179764
0.52	Remote Similarity	NPC143396
0.5135	Remote Similarity	NPC155263
0.5116	Remote Similarity	NPC91495
0.5116	Remote Similarity	NPC70387

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC1504 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6307
0.1-0.2	2579
0.2-0.3	214
0.3-0.4	22
0.4-0.5	12
0.5-0.6	8
0.6-0.7	4
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
0.7273	Intermediate Similarity	NPD4246	Phase 2
0.7111	Intermediate Similarity	NPD4247	Clinical (unspecified phase)
0.6579	Remote Similarity	NPD3195	Phase 2
0.6579	Remote Similarity	NPD3196	Approved
0.6279	Remote Similarity	NPD3194	Phase 4
0.6098	Remote Similarity	NPD4266	Phase 2
0.5476	Remote Similarity	NPD3173	Phase 4
0.5455	Remote Similarity	NPD4269	Phase 4
0.5455	Remote Similarity	NPD4270	Approved
0.5405	Remote Similarity	NPD2270	Pre-clinical
0.5405	Remote Similarity	NPD633	Phase 3
0.5405	Remote Similarity	NPD9448	Phase 2
0.537	Remote Similarity	NPD4271	Phase 4
0.5349	Remote Similarity	NPD3172	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