NPASS Compound

Natural Product: NPC185634

Natural Product ID	NPC185634
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	QOFWRHWADNWKSU-LRXIOGKNSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	10455173
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001534] Quinone and hydroquinone lipids [CHEMONTID:0001546] Vitamin E compounds [CHEMONTID:0002092] Tocotrienols

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 69 70 0 0 0 0 0 0 0 0999 V2000 3.8069 -2.3928 1.1161 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3750 -1.1983 1.7952 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6271 -0.0982 1.8292 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2930 -0.0975 1.2091 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1548 0.9261 0.1006 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7710 0.8151 -0.4286 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0312 1.8508 -0.3774 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4350 1.8167 -0.8887 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3714 2.1310 0.2801 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7912 2.0860 -0.2866 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.9517 3.1093 -1.3887 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7602 2.4534 0.8163 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1780 2.1042 0.4023 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1669 0.6216 0.1539 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2880 -0.1371 0.5105 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2670 -1.4988 0.2779 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1459 -2.0842 -0.2991 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0443 -1.3552 -0.6521 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8283 -1.9421 -1.2703 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0698 0.0133 -0.4166 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9733 0.7666 -0.7635 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.3717 -2.2877 0.6225 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3266 -0.4703 -1.0050 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7109 -1.2800 2.4090 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7447 -1.5891 1.3553 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7351 -0.5096 0.3505 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5796 -0.7524 -0.9284 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4067 -2.1306 -1.4374 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5751 0.3734 -1.8843 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7188 1.5188 -1.4499 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4102 0.1208 -3.2439 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4607 -2.1976 0.0982 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9578 -2.7895 1.7145 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5654 -3.2105 1.0677 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9972 0.7961 2.3118 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5539 0.2182 2.0029 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9513 -1.0598 0.8305 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3336 1.9471 0.5051 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8913 0.7674 -0.7114 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3372 2.7743 0.0542 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6723 0.8318 -1.3303 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5084 2.5689 -1.6891 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1274 3.0867 0.7384 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2949 1.2598 0.9655 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1106 3.8330 -1.2774 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9787 2.6309 -2.3842 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8803 3.7145 -1.2552 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5648 1.9015 1.7595 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6591 3.5524 0.9660 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8524 2.3674 1.2270 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4837 2.5941 -0.5308 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1477 0.3672 0.9621 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1551 -3.1624 -0.4721 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0240 -2.9379 -1.7158 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1101 -2.1173 -0.4224 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3568 -1.2270 -1.9506 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.1439 -2.2772 -0.0338 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3946 -1.0146 -0.3614 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1992 -1.1556 -1.1664 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1500 -0.3576 -2.0039 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6658 -2.0718 3.1872 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9483 -0.3132 2.9289 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5048 -2.5530 0.8662 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7492 -1.6731 1.8377 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8595 0.5447 0.6464 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2095 -2.7837 -1.0025 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3954 -2.5144 -1.2645 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5348 -2.0863 -2.5600 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9385 0.8635 -3.7775 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 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 10 9 1 1 10 11 1 0 10 12 1 0 12 13 1 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 1 0 18 20 2 0 20 21 1 0 16 22 1 0 6 23 1 0 2 24 1 0 24 25 1 0 25 26 1 0 26 27 2 0 27 28 1 0 27 29 1 0 29 30 2 0 29 31 1 0 21 10 1 0 20 14 1 0 1 32 1 0 1 33 1 0 1 34 1 0 3 35 1 0 4 36 1 0 4 37 1 0 5 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 11 45 1 0 11 46 1 0 11 47 1 0 12 48 1 0 12 49 1 0 13 50 1 0 13 51 1 0 15 52 1 0 17 53 1 0 19 54 1 0 19 55 1 0 19 56 1 0 22 57 1 0 23 58 1 0 23 59 1 0 23 60 1 0 24 61 1 0 24 62 1 0 25 63 1 0 25 64 1 0 26 65 1 0 28 66 1 0 28 67 1 0 28 68 1 0 31 69 1 0 M END

Standard InCHIKey	QOFWRHWADNWKSU-LRXIOGKNSA-N
Standard InCHI	InChI=1S/C27H38O4/c1-19(11-7-13-21(3)26(29)30)9-6-10-20(2)12-8-15-27(5)16-14-23-18-24(28)17-22(4)25(23)31-27/h9,12-13,17-18,28H,6-8,10-11,14-16H2,1-5H3,(H,29,30)/b19-9+,20-12+,21-13+/t27-/m1/s1
SMILES	C/C(=CCC/C(=C/CC[C@]1(C)CCc2cc(cc(C)c2O1)O)/C)/CC/C=C(C)/C(=O)O

Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO19087	Garcinia kola	Species	Clusiaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[32644811]
NPO19087	Garcinia kola	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO19087	Garcinia kola	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19087	Garcinia kola	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19087	Garcinia kola	Species	Clusiaceae	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
Kd	1
EC50	1
IC50	4
Activity	4
MIC	2
MBC	2

Activity Type	# Activity
Individual protein	8
Organism	4
Others	2

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT543	Individual protein	Pregnane X receptor	Homo sapiens	Kd	=	330.0	nM	PMID[32160459]
NPT543	Individual protein	Pregnane X receptor	Homo sapiens	EC50	=	1300.0	nM	PMID[32160459]
NPT570	Individual protein	Arachidonate 5-lipoxygenase	Homo sapiens	IC50	=	57.0	nM	PMID[32668380]
NPT570	Individual protein	Arachidonate 5-lipoxygenase	Homo sapiens	IC50	=	345.0	nM	PMID[32668380]
NPT570	Individual protein	Arachidonate 5-lipoxygenase	Homo sapiens	Activity	=	1.4	%	PMID[34279935]
NPT570	Individual protein	Arachidonate 5-lipoxygenase	Homo sapiens	IC50	=	60.0	nM	PMID[34279935]
NPT570	Individual protein	Arachidonate 5-lipoxygenase	Homo sapiens	IC50	=	350.0	nM	PMID[34279935]
NPT570	Individual protein	Arachidonate 5-lipoxygenase	Homo sapiens	Activity	=	0.4	%	PMID[34279935]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1127	Organism	Porphyromonas gingivalis	Porphyromonas gingivalis	MIC	=	31300.0	nM	PMID[32644811]
NPT1127	Organism	Porphyromonas gingivalis	Porphyromonas gingivalis	MBC	=	250.0	uM	PMID[32644811]
NPT27	Others	Unspecified	n.a.	Activity	=	33.0	%	PMID[32160459]
NPT27	Others	Unspecified	n.a.	Activity	=	100.0	%	PMID[32160459]
NPT1483	Organism	Streptococcus sobrinus	Streptococcus sobrinus	MIC	=	31300.0	nM	PMID[32644811]
NPT1483	Organism	Streptococcus sobrinus	Streptococcus sobrinus	MBC	=	62.5	uM	PMID[32644811]

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 NPC185634 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	18019
0.1-0.2	29922
0.2-0.3	1735
0.3-0.4	130
0.4-0.5	12
0.5-0.6	13
0.6-0.7	19
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
0.7727	Intermediate Similarity	NPC479050
0.7705	Intermediate Similarity	NPC69539
0.7536	Intermediate Similarity	NPC474237
0.75	Intermediate Similarity	NPC32152
0.7231	Intermediate Similarity	NPC147896
0.6923	Remote Similarity	NPC479051
0.6912	Remote Similarity	NPC610467
0.6761	Remote Similarity	NPC59654
0.6714	Remote Similarity	NPC232295
0.6714	Remote Similarity	NPC611336
0.6625	Remote Similarity	NPC479052
0.662	Remote Similarity	NPC204535
0.662	Remote Similarity	NPC474131
0.662	Remote Similarity	NPC46586
0.662	Remote Similarity	NPC609807
0.6528	Remote Similarity	NPC271832
0.6528	Remote Similarity	NPC600119
0.6528	Remote Similarity	NPC601388
0.6351	Remote Similarity	NPC610755
0.6267	Remote Similarity	NPC474130
0.625	Remote Similarity	NPC276962
0.625	Remote Similarity	NPC190086
0.6232	Remote Similarity	NPC606596
0.6	Remote Similarity	NPC196621
0.5844	Remote Similarity	NPC474246
0.5797	Remote Similarity	NPC45663
0.5769	Remote Similarity	NPC474143
0.5753	Remote Similarity	NPC483459
0.5753	Remote Similarity	NPC483457
0.5753	Remote Similarity	NPC483456
0.5753	Remote Similarity	NPC483458
0.5714	Remote Similarity	NPC95034
0.5714	Remote Similarity	NPC142087
0.5714	Remote Similarity	NPC603704
0.5443	Remote Similarity	NPC475880
0.5195	Remote Similarity	NPC483461
0.5063	Remote Similarity	NPC609806

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC185634 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4092
0.1-0.2	4969
0.2-0.3	88
0.3-0.4	0
0.4-0.5	0
0.5-0.6	1
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
0.5652	Remote Similarity	NPD6671	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