NPASS Compound

Natural Product: NPC471216

Natural Product ID	NPC471216
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	LGITXCALUZAZQD-LHECGIGESA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL2391537
PubChem CID	71577606
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids

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 70 73 0 0 0 0 0 0 0 0999 V2000 -1.3140 -2.5267 -2.2412 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1716 -1.8307 -1.6079 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8356 -2.9135 -1.2335 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1340 -2.1722 -0.9944 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8865 -1.2521 0.1769 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1811 -0.6857 0.6068 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0419 0.4019 1.6626 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6903 0.2500 2.2710 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6349 0.5526 1.2200 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7954 -0.2592 -0.0383 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5103 -0.9668 -0.4176 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1257 -1.6971 0.7097 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4502 -1.0053 0.9307 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5137 0.0062 -0.1404 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3677 0.0204 -0.8595 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8396 1.3595 0.5076 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5060 2.0692 -0.6511 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7201 1.1493 -1.6495 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7664 -0.1150 -1.0161 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9064 -0.2712 -0.2747 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.6071 -1.3726 -0.7641 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6691 2.6681 -0.2208 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5984 4.0383 -0.3001 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0804 0.7065 -1.1673 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2829 1.6863 1.1499 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2470 2.5549 1.6085 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9666 2.1450 2.5733 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4438 3.8968 1.0172 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9711 -1.8184 1.2821 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0560 -0.1444 -0.4764 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9748 -2.9653 -1.4703 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8611 -1.9328 -2.9945 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9046 -3.3979 -2.8145 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3386 -1.1674 -2.3441 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8886 -3.5954 -2.0996 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5322 -3.4793 -0.3532 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3770 -1.6487 -1.9271 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9360 -2.8737 -0.6896 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5264 -1.9285 1.0106 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7894 0.2610 2.4961 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5867 -0.7490 2.7042 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5789 1.0295 3.0544 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6821 1.6481 1.0444 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3300 0.3616 1.7320 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3611 -2.7691 0.4758 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5111 -1.7320 1.6320 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3074 -1.7042 0.8719 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5163 -0.5802 1.9755 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9649 1.8802 0.8863 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6005 1.1281 1.2886 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7988 2.8803 -0.9574 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6522 -0.8742 -1.8130 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5520 -1.5513 -0.1951 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8297 -1.2424 -1.8571 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0149 -2.3076 -0.6959 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4212 4.4213 -1.3307 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5699 4.4413 0.0992 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7440 4.4152 0.3162 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1695 0.8826 -1.8117 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3615 1.7187 -0.8113 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8469 0.3236 -1.8672 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8864 4.6950 1.5414 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0811 3.8717 -0.0424 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5214 4.1784 0.9524 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7526 -1.3563 1.9413 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3109 -2.3962 1.9608 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5028 -2.4377 0.5455 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1203 -0.7499 -1.3789 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1053 -0.1161 -0.0538 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8383 0.9446 -0.6849 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 14 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 17 22 1 0 22 23 1 0 10 24 1 0 7 25 1 0 25 26 1 0 26 27 2 0 26 28 1 0 6 29 1 0 6 30 1 0 11 2 1 0 10 5 1 0 15 11 1 0 19 14 1 0 1 31 1 0 1 32 1 0 1 33 1 0 2 34 1 0 3 35 1 0 3 36 1 0 4 37 1 0 4 38 1 0 5 39 1 0 7 40 1 0 8 41 1 0 8 42 1 0 9 43 1 0 9 44 1 0 12 45 1 0 12 46 1 0 13 47 1 0 13 48 1 0 16 49 1 0 16 50 1 0 17 51 1 0 19 52 1 0 21 53 1 0 21 54 1 0 21 55 1 0 23 56 1 0 23 57 1 0 23 58 1 0 24 59 1 0 24 60 1 0 24 61 1 0 28 62 1 0 28 63 1 0 28 64 1 0 29 65 1 0 29 66 1 0 29 67 1 0 30 68 1 0 30 69 1 0 30 70 1 0 M END

Standard InCHIKey	LGITXCALUZAZQD-LHECGIGESA-N
Standard InCHI	InChI=1S/C24H40O6/c1-15-8-9-17-21(3,4)18(28-16(2)25)10-11-22(17,5)24(15)13-12-23(30-24)14-19(26-6)29-20(23)27-7/h15,17-20H,8-14H2,1-7H3/t15-,17+,18+,19+,20-,22+,23+,24-/m1/s1
SMILES	CC1CCC2C(C(CCC2(C13CCC4(O3)CC(OC4OC)OC)C)OC(=O)C)(C)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	424.28	Volume:	439.539 ? Van der Waals volume.
Dense:	0.965	LogP:	3.19 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.266 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.139 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	22.0
TPSA:	63.22 ? Topological Polar Surface Area.	H-Bond Acceptor:	6.0
H-Bond Donor:	0.0	Rings:	4.0
Heavy Atoms:	6.0

MedChem Properties

QED Drug-Likeness Score:	0.624	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.674	Fsp³:	0.958
MCE-18:	110.426 ? 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:	0.013	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.006 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.017 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.431	Promiscuous compounds:	0.017

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.027	MDCK Permeability:	-4.772
Pgp-inhibitor:	0.829	Pgp-substrate:	0.026
PAMPA:	0.059 ? 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):	0.007
20% Bioavailability (F20%):	0.014	30% Bioavailability (F30%):	0.083
50% Bioavailability (F50%):	0.792

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.221	MRP1:	0.999
Plasma Protein Binding (PPB):	93.894%	Volume Distribution (VD):	0.652
Fu:	5.471% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.004
OATP1B3 inhibitor:	0.258	BCRP inhibitor:	0.002
BSEP inhibitor:	0.995

ADMET: Metabolism

CYP1A2-inhibitor:	0.417	CYP1A2-substrate:	0.276
CYP2C19-inhibitor:	1.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.726	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.927	CYP2D6-substrate:	0.001
CYP3A4-inhibitor:	0.263	CYP3A4-substrate:	0.169
CYP2B6-substrate:	1.0	CYP2C8-inhibitor:	0.001
HLM stability:	0.987 ? 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):

9.631

Half-life (T1/2):

1.036

ADMET: Toxicity

hERG Blockers:	0.155	hERG Blockers (10um):	0.568
Human Hepatotoxicity (H-HT):	0.453	Drug-induced Liver Injury (DILI):	0.443
AMES Toxicity:	0.41	Rat Oral Acute Toxicity:	0.331
Maximum Recommended Daily Dose:	0.486	Skin Sensitization:	0.847
Carcinogencity:	0.361	Eye Corrosion:	0.029
Eye Irritation:	0.467	Respiratory Toxicity:	0.451
Drug-induced Neurotoxicity:	0.593	Ototoxicity:	0.541
Hematotoxicity:	0.13	Drug-induced Nephrotoxicity:	0.067
Genotoxicity:	0.013	RPMI-8226 Immunitoxicity:	0.065
A549 Cytotoxicity:	0.115	Hek293 Cytotoxicity:	0.227
BCF:	1.533 ? 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:	4.176 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.908 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.115 ? 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
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	fruit	n.a.	PMID[15577254]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15621610]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	fruits	n.a.	n.a.	PMID[23327905]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[28453270]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21373	Vitex trifolia	Species	Lamiaceae	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

Activity Type	# Activity
IC50	4

Activity Type	# Activity
Cell line	4

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
NPT994	Cell line	ZR-75-30	Homo sapiens	IC50	<	5.0	ug.mL-1	PMID[24913558]
NPT116	Cell line	HL-60	Homo sapiens	IC50	<	5.0	ug.mL-1	PMID[22608855]
NPT393	Cell line	HCT-116	Homo sapiens	IC50	<	5.0	ug.mL-1	PMID[19546358]
NPT81	Cell line	A549	Homo sapiens	IC50	<	5.0	ug.mL-1	PMID[23398362]

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 NPC471216 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	22795
0.1-0.2	25208
0.2-0.3	1802
0.3-0.4	44
0.4-0.5	1
0.5-0.6	6
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	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC471217
0.7193	Intermediate Similarity	NPC221993
0.5741	Remote Similarity	NPC55508
0.5645	Remote Similarity	NPC71541
0.5484	Remote Similarity	NPC481388
0.5397	Remote Similarity	NPC18953
0.5238	Remote Similarity	NPC106332
0.5161	Remote Similarity	NPC264546

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC471216 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7215
0.1-0.2	1903
0.2-0.3	32
0.3-0.4	0
0.4-0.5	0
0.5-0.6	0
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
		NPD

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