NPASS Compound

Natural Product: NPC47634

Natural Product ID	NPC47634
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	COVMVPHACFXMAX-FYBISLNESA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3809573
PubChem CID	16078251
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000123] Benzopyrans [CHEMONTID:0003410] 1-benzopyrans [CHEMONTID:0002817] Dibenzopyrans [CHEMONTID:0000200] Xanthenes [CHEMONTID:0000204] Xanthones [CHEMONTID:0003521] Pyranoxanthones

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 77 82 0 0 0 0 0 0 0 0999 V2000 -3.4235 3.8769 0.7017 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2585 2.7725 -0.3159 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1700 2.0271 -0.2195 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9013 0.8969 -1.1780 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7127 -0.3409 -0.3556 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7925 -0.9854 0.1992 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6064 -2.1355 0.9637 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7681 -2.7936 1.5367 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9738 -2.3323 1.3511 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2321 -1.1290 0.5582 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9450 -0.1510 1.5160 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2208 -1.5066 -0.5493 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0842 -0.5283 0.0253 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3100 -2.5700 1.1215 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2316 -1.9292 0.5693 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1422 -2.3898 0.7348 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3782 -3.4150 1.4086 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2551 -1.6768 0.1280 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5338 -1.9945 0.2792 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3884 -1.4448 -0.8494 C 0 0 1 0 0 0 0 0 0 0 0 0 3.5871 -1.7349 -2.1020 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3767 -0.8668 -2.1984 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6167 0.5039 -2.7438 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8536 0.5680 -3.6172 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4332 0.9108 -3.5895 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7277 1.3716 -1.6796 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9460 0.5951 -0.5238 C 0 0 2 0 0 0 0 0 0 0 0 0 2.7316 1.4170 0.7153 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9588 0.6491 1.9411 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8877 0.8399 2.8515 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9283 -0.0810 4.0394 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8640 1.8834 2.7338 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9904 2.7184 1.8166 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7992 1.9752 3.7908 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3206 0.0441 -0.6222 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3274 0.7239 -0.5293 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9630 -0.5143 -0.7423 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6404 -0.1016 -0.7697 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3931 -0.7927 -0.1885 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1065 -3.7245 1.8871 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2949 2.5927 -1.3590 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8662 3.4868 1.6323 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4117 4.2485 0.9353 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0526 4.6589 0.2224 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4373 2.2353 0.5829 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0095 1.1007 -1.7728 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7588 0.7939 -1.8652 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6064 -3.7083 2.1430 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8246 -2.8459 1.7923 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0241 -0.3739 1.4450 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5814 -0.3386 2.5611 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7149 0.8827 1.2569 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1850 -0.7370 -1.3222 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0307 -2.5294 -0.9181 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2278 -1.4963 -0.0717 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9362 -2.5630 1.0828 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3926 -1.8427 -0.8486 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2071 -2.7915 -1.9662 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2020 -1.7815 -3.0145 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4971 -1.3798 -2.6158 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0255 1.6554 -3.8272 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7522 0.1709 -3.1489 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6210 0.1151 -4.6021 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7976 1.2776 -4.5715 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7743 0.0307 -3.6983 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8839 1.7376 -3.0850 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2882 2.3470 0.6566 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6333 1.7335 0.7753 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2733 -0.2036 2.1644 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9864 -0.0692 4.5909 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7378 0.2182 4.7077 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1443 -1.1146 3.6902 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4956 2.7301 3.7498 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4496 -4.6210 1.5469 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9011 3.5296 -1.4892 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8078 2.4454 -2.3467 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9840 1.7703 -1.1076 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 3 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 10 12 1 0 10 13 1 0 7 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 16 18 1 0 18 19 2 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 23 25 1 0 23 26 1 0 26 27 1 0 27 28 1 1 28 29 1 0 29 30 2 0 30 31 1 0 30 32 1 0 32 33 2 0 32 34 1 0 27 35 1 0 35 36 2 0 27 37 1 0 37 38 1 6 38 39 1 0 14 40 1 0 2 41 1 0 39 5 2 0 13 6 1 0 39 15 1 0 37 18 1 0 35 20 1 0 37 22 1 0 1 42 1 0 1 43 1 0 1 44 1 0 3 45 1 0 4 46 1 0 4 47 1 0 8 48 1 0 9 49 1 0 11 50 1 0 11 51 1 0 11 52 1 0 12 53 1 0 12 54 1 0 12 55 1 0 19 56 1 0 20 57 1 6 21 58 1 0 21 59 1 0 22 60 1 0 24 61 1 0 24 62 1 0 24 63 1 0 25 64 1 0 25 65 1 0 25 66 1 0 28 67 1 0 28 68 1 0 29 69 1 0 31 70 1 0 31 71 1 0 31 72 1 0 34 73 1 0 40 74 1 0 41 75 1 0 41 76 1 0 41 77 1 0 M END

Standard InCHIKey	COVMVPHACFXMAX-FYBISLNESA-N
Standard InCHI	InChI=1S/C33H36O8/c1-16(2)8-9-20-26-19(11-12-30(4,5)39-26)24(34)23-25(35)21-14-18-15-22-31(6,7)41-32(28(18)36,13-10-17(3)29(37)38)33(21,22)40-27(20)23/h8,10-12,14,18,22,34H,9,13,15H2,1-7H3,(H,37,38)/b17-10-/t18-,22?,32+,33-/m0/s1
SMILES	CC(=CCc1c2c(C=CC(C)(C)O2)c(c2C(=O)C3=C[C@H]4CC5C(C)(C)O[C@](C/C=C(/C)C(=O)O)(C4=O)[C@]35Oc12)O)C

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
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	fruit	n.a.	PMID[17117343]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	latex	n.a.	PMID[17117343]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	resin	n.a.	n.a.	PMID[19072548]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20815207]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	bark	n.a.	PMID[21319773]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	leaf	n.a.	PMID[21319773]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	root	n.a.	PMID[21319773]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21486005]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	leaf	n.a.	PMID[22207282]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	root	n.a.	PMID[23806866]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	root bark	University of Veterinary and Pharmaceutical Sciences Brno (UVPS Brno), Brno, Czech Republic	2011-APR	PMID[24901948]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	Konya, Turkey	2007-APR	PMID[24901948]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	leaves	Chungbuk, Korea	n.a.	PMID[25935644]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	root	n.a.	PMID[25981820]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	latex	n.a.	PMID[27294120]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	Root barks	n.a.	n.a.	PMID[3097265]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13310	Garcinia hanburyi	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
IZ	2
MIC	2
IC50	2
MBC	2

Activity Type	# Activity
Cell line	2
Organism	6

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
NPT81	Cell line	A549	Homo sapiens	IC50	=	3500.0	nM	PMID[27216998]
NPT71	Cell line	HEK293	Homo sapiens	IC50	=	2330.0	nM	PMID[27216998]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	IZ	=	19.23	mm	PMID[27216998]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	12500.0	nM	PMID[27216998]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	IZ	=	19.52	mm	PMID[27216998]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MBC	=	12.5	uM	PMID[27216998]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MBC	=	25.0	uM	PMID[27216998]

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 NPC47634 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	10933
0.1-0.2	37447
0.2-0.3	1356
0.3-0.4	66
0.4-0.5	22
0.5-0.6	16
0.6-0.7	5
0.7-0.8	0
0.8-0.85	4
0.85-0.9	3
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC40089
0.8621	High Similarity	NPC158329
0.8621	High Similarity	NPC55422
0.8621	High Similarity	NPC75141
0.8171	Intermediate Similarity	NPC131578
0.8171	Intermediate Similarity	NPC611483
0.8152	Intermediate Similarity	NPC476146
0.8068	Intermediate Similarity	NPC610447
0.7701	Intermediate Similarity	NPC223413
0.7263	Intermediate Similarity	NPC189689
0.7113	Intermediate Similarity	NPC476216
0.7041	Intermediate Similarity	NPC41598
0.6771	Remote Similarity	NPC611384
0.6667	Remote Similarity	NPC476199
0.66	Remote Similarity	NPC476229
0.66	Remote Similarity	NPC476152
0.6346	Remote Similarity	NPC162248
0.5922	Remote Similarity	NPC476210
0.5769	Remote Similarity	NPC601073
0.5769	Remote Similarity	NPC609328
0.57	Remote Similarity	NPC476159
0.5667	Remote Similarity	NPC94796
0.5667	Remote Similarity	NPC611777
0.5408	Remote Similarity	NPC286422
0.5408	Remote Similarity	NPC603867
0.54	Remote Similarity	NPC476255
0.5368	Remote Similarity	NPC608101
0.5333	Remote Similarity	NPC102810
0.5273	Remote Similarity	NPC476139
0.5213	Remote Similarity	NPC607281
0.52	Remote Similarity	NPC63514
0.5094	Remote Similarity	NPC601782
0.5049	Remote Similarity	NPC476196

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC47634 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3306
0.1-0.2	5810
0.2-0.3	34
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