NPASS Compound

Natural Product: NPC607625

Natural Product ID	NPC607625
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	PILMPTUAXYPAME-KKYGLDRZSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL2203591
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 77 80 0 0 0 0 0 0 0 0999 V2000 6.3929 -1.0413 2.2374 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6841 -0.0125 1.1779 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0716 -0.0551 0.0063 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0912 -1.1065 -0.2931 C 0 0 1 0 0 0 0 0 0 0 0 0 5.3036 -2.2980 0.3890 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6591 -0.6962 -0.0622 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2673 0.4784 -0.9117 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3848 0.2352 -2.3828 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0230 1.1518 -0.4571 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6558 2.3227 -1.3263 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1947 2.0849 -1.6470 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2913 2.4075 -2.6719 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3014 1.4316 -0.4512 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.2338 2.3898 0.7182 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6429 0.8473 -0.4788 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8797 -0.1644 0.3839 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8304 -0.6092 1.2798 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0608 -1.3275 2.2597 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6058 -0.2242 1.0753 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7968 0.3466 -0.3082 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4937 -0.6855 -1.3052 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2233 -0.8426 0.3812 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.1252 -1.8255 -0.8046 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4671 -1.6832 1.5834 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8773 -2.2814 1.4432 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8047 -1.1188 1.5054 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6024 -0.9725 2.4067 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.6651 -0.1565 0.3666 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4017 1.1080 0.7591 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3981 -0.7639 -0.8034 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2507 0.1856 0.0836 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.0168 0.6015 -1.3767 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7233 1.3381 -1.3275 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6350 2.3565 -2.0268 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6450 1.0506 1.4176 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2457 1.1208 2.5210 O 0 0 0 0 0 0 0 0 0 0 0 0 7.8922 1.9785 0.4296 O 0 0 0 0 0 0 0 0 0 0 0 0 5.3290 -1.1658 2.4284 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9387 -1.9954 2.0269 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8434 -0.6558 3.1767 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3138 0.7056 -0.7226 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1821 -1.3681 -1.3886 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4234 -3.0746 -0.1843 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0449 -1.5929 -0.2050 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5770 -0.3749 0.9966 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1012 1.2259 -0.7089 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5034 0.5189 -2.9738 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5520 -0.8467 -2.5677 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2480 0.7438 -2.8578 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2367 1.5660 0.5603 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7030 3.3059 -0.8328 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2593 2.4045 -2.2464 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6216 1.9579 1.6561 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7254 2.8670 0.8801 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9568 3.2164 0.4563 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1928 -1.1494 1.2463 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8717 0.5764 1.7961 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1796 -0.3029 -2.1316 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1312 -1.5042 -0.8355 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3088 -1.1926 -1.8029 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0998 -2.0858 -1.2122 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6867 -2.7858 -0.4183 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4117 -1.4785 -1.5684 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8098 -2.5801 1.5256 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4621 -1.1687 2.5465 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9742 -2.8644 0.5126 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0273 -2.9357 2.3256 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6496 1.6602 -0.1607 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3024 0.8402 1.3399 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7117 1.7703 1.3553 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9536 -0.5152 -1.7764 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4876 -1.8644 -0.6946 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4584 -0.3871 -0.8354 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9828 1.1031 0.6880 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9424 -0.2475 -2.0594 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8499 1.2391 -1.7337 H 0 0 0 0 0 0 0 0 0 0 0 0 8.3682 2.8645 0.6092 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 4 6 1 0 6 7 1 0 7 8 1 0 7 9 1 0 9 10 1 0 10 11 1 0 11 12 2 0 11 13 1 0 13 14 1 1 13 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 17 19 1 0 19 20 1 0 20 21 1 6 16 22 1 0 22 23 1 6 22 24 1 0 24 25 1 0 25 26 1 0 26 27 2 0 26 28 1 0 28 29 1 0 28 30 1 0 28 31 1 0 31 32 1 0 32 33 1 0 33 34 2 0 2 35 1 0 35 36 2 0 35 37 1 0 20 9 1 0 31 22 1 0 20 13 1 0 33 15 1 0 1 38 1 0 1 39 1 0 1 40 1 0 3 41 1 0 4 42 1 6 5 43 1 0 6 44 1 0 6 45 1 0 7 46 1 1 8 47 1 0 8 48 1 0 8 49 1 0 9 50 1 1 10 51 1 0 10 52 1 0 14 53 1 0 14 54 1 0 14 55 1 0 19 56 1 0 19 57 1 0 21 58 1 0 21 59 1 0 21 60 1 0 23 61 1 0 23 62 1 0 23 63 1 0 24 64 1 0 24 65 1 0 25 66 1 0 25 67 1 0 29 68 1 0 29 69 1 0 29 70 1 0 30 71 1 0 30 72 1 0 30 73 1 0 31 74 1 1 32 75 1 0 32 76 1 0 37 77 1 0 M END

Standard InCHIKey	PILMPTUAXYPAME-KKYGLDRZSA-N
Standard InCHI	InChI=1S/C30H40O7/c1-15(10-17(31)11-16(2)26(36)37)18-12-23(35)30(7)25-19(32)13-21-27(3,4)22(34)8-9-28(21,5)24(25)20(33)14-29(18,30)6/h11,15,17-18,21,31H,8-10,12-14H2,1-7H3,(H,36,37)/b16-11+/t15-,17+,18-,21+,28+,29-,30+/m1/s1
SMILES	C/C(=C[C@@H](O)C[C@@H](C)[C@H]1CC(=O)[C@@]2(C)C3=C(C(=O)C[C@]12C)[C@@]1(C)CCC(=O)C(C)(C)[C@@H]1CC3=O)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
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.phytochem.2005.10.025]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	fruit body	n.a.	PMID[11520245]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12045343]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14695801]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1791484]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	spore	n.a.	PMID[18827358]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	fruiting bodies	Nagano, Japan	2008-MAY	PMID[20039640]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20384295]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	fruiting bodies	n.a.	n.a.	PMID[20702092]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	fruiting bodies	n.a.	n.a.	PMID[21924611]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22014750]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	fruit body	n.a.	PMID[22044278]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	fruiting body	n.a.	n.a.	PMID[22047696]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26222905]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	fruit body	n.a.	PMID[9635497]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	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	3

Activity Type	# Activity
Cell line	3

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
NPT515	Cell line	SGC-7901	Homo sapiens	IC50	=	7250.0	nM	PMID[23092389]
NPT181	Cell line	Bel-7402	Homo sapiens	IC50	=	7250.0	nM	PMID[23092389]
NPT168	Cell line	P388	Mus musculus	IC50	=	7250.0	nM	PMID[23092389]

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 NPC607625 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	17789
0.1-0.2	29436
0.2-0.3	2338
0.3-0.4	214
0.4-0.5	52
0.5-0.6	24
0.6-0.7	3
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8281	Intermediate Similarity	NPC287833
0.6269	Remote Similarity	NPC209882
0.6269	Remote Similarity	NPC607131
0.6056	Remote Similarity	NPC37646
0.5909	Remote Similarity	NPC271784
0.589	Remote Similarity	NPC295244
0.5811	Remote Similarity	NPC243525
0.5811	Remote Similarity	NPC40765
0.5781	Remote Similarity	NPC473038
0.5753	Remote Similarity	NPC479661
0.5556	Remote Similarity	NPC162703
0.5507	Remote Similarity	NPC249212
0.5429	Remote Similarity	NPC469561
0.5429	Remote Similarity	NPC484799
0.5352	Remote Similarity	NPC11711
0.5342	Remote Similarity	NPC476174
0.5342	Remote Similarity	NPC3772
0.5333	Remote Similarity	NPC241156
0.5333	Remote Similarity	NPC488419
0.5333	Remote Similarity	NPC600288
0.5256	Remote Similarity	NPC293753
0.5176	Remote Similarity	NPC472935
0.5132	Remote Similarity	NPC264404
0.5128	Remote Similarity	NPC121339
0.5128	Remote Similarity	NPC73506
0.5067	Remote Similarity	NPC255809
0.5065	Remote Similarity	NPC106557
0.5063	Remote Similarity	NPC604630

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC607625 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5499
0.1-0.2	3567
0.2-0.3	84
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