NPASS Compound

Natural Product: NPC607477

Natural Product ID	NPC607477
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	SHNUOEZKLYTPJU-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL5284131
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 56 61 0 0 0 0 0 0 0 0999 V2000 -6.1479 1.7535 0.4751 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0127 0.5349 0.7472 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7291 0.0091 0.7075 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5711 0.8232 0.3656 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3418 2.0837 0.8764 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2319 2.8267 0.5287 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2941 2.3298 -0.3571 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1658 3.0986 -0.7052 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5129 1.0710 -0.8734 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6064 0.5481 -1.7528 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7000 0.2991 -1.4687 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5594 -0.1477 -2.4685 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8953 -0.4019 -2.1727 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3979 -0.2215 -0.9015 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7913 -0.4784 -0.5589 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1447 -1.1665 0.5802 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4118 -1.3998 0.8912 O 0 0 0 0 0 0 0 0 0 0 0 0 7.3907 -0.9888 0.1329 C 0 0 0 0 0 0 0 0 0 0 0 0 8.7098 -1.2546 0.4953 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0164 -2.1402 1.9713 Cl 0 0 0 0 0 0 0 0 0 0 0 0 9.7194 -0.8096 -0.3224 C 0 0 0 0 0 0 0 0 0 0 0 0 11.0485 -1.0789 0.0453 O 0 0 0 0 0 0 0 0 0 0 0 0 9.4610 -0.1080 -1.4907 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1495 0.1474 -1.8362 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1313 -0.2909 -1.0290 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8037 -0.0306 -1.3817 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5585 0.6058 -2.4407 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5289 0.2227 0.0784 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1955 0.4802 -0.2008 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6301 0.3372 -0.5163 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6354 -1.3409 1.0161 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6793 -2.0736 1.3240 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9053 -1.6078 1.3705 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.9871 -2.4258 1.7035 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.2720 -1.9008 1.7436 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.3757 -2.6837 2.0710 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.4551 -0.5557 1.4476 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.3641 0.2454 1.1175 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0846 -0.2713 1.0761 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0340 2.5103 1.5616 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0620 3.8220 0.9394 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1045 3.5499 -1.6036 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1863 -0.2977 -3.4798 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5892 -0.7502 -2.9274 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3748 -1.5387 1.2594 H 0 0 0 0 0 0 0 0 0 0 0 0 11.2691 -1.1760 1.0419 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3007 0.2127 -2.0874 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9101 0.6866 -2.7312 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9276 0.3646 1.0818 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5455 0.8192 0.5871 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7829 -0.6629 -0.9409 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6198 -1.7672 0.9871 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8339 -3.4786 1.9339 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.2944 -2.4606 1.7149 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.4684 -0.1694 1.4858 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.5149 1.2881 0.8892 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 1 0 4 5 2 0 5 6 1 0 6 7 2 0 7 8 1 0 7 9 1 0 9 10 1 0 10 11 1 0 11 12 2 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 1 0 18 19 2 0 19 20 1 0 19 21 1 0 21 22 1 0 21 23 2 0 23 24 1 0 24 25 2 0 25 26 1 0 26 27 2 0 14 28 1 0 28 29 2 0 9 30 2 0 3 31 2 0 31 32 1 0 32 33 1 0 33 34 2 0 34 35 1 0 35 36 1 0 35 37 2 0 37 38 1 0 38 39 2 0 39 2 1 0 30 4 1 0 39 33 1 0 29 11 1 0 26 15 1 0 25 18 1 0 5 40 1 0 6 41 1 0 8 42 1 0 12 43 1 0 13 44 1 0 16 45 1 0 22 46 1 0 23 47 1 0 24 48 1 0 28 49 1 0 29 50 1 0 30 51 1 0 31 52 1 0 34 53 1 0 36 54 1 0 37 55 1 0 38 56 1 0 M END

Standard InCHIKey	SHNUOEZKLYTPJU-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C30H17ClO8/c31-27-24(34)10-8-20-29(36)21(14-38-30(20)27)15-1-5-18(6-2-15)39-26-11-16(3-9-23(26)33)22-13-37-25-12-17(32)4-7-19(25)28(22)35/h1-14,32-34H
SMILES	O=c1c(-c2ccc(O)c(Oc3ccc(-c4coc5c(Cl)c(O)ccc5c4=O)cc3)c2)coc2cc(O)ccc12

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
NPO43802	Streptomyces sp. HDN154127	Genus	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]

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
MIC	14

Activity Type	# Activity
Organism	14

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
NPT5492	Organism	Proteus sp.	Proteus sp.	MIC	>	50000.0	nM	PMID[36535025]
NPT29703	Organism	Mycolicibacterium phlei	Mycolicibacterium phlei	MIC	>	50000.0	nM	PMID[36535025]
NPT20	Organism	Candida albicans	Candida albicans	MIC	=	1600.0	nM	PMID[36535025]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	=	800.0	nM	PMID[36535025]
NPT565	Organism	Vibrio parahaemolyticus	Vibrio parahaemolyticus	MIC	=	800.0	nM	PMID[36535025]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>	50000.0	nM	PMID[36535025]
NPT314	Organism	Bacillus cereus	Bacillus cereus	MIC	>	50000.0	nM	PMID[36535025]

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 NPC607477 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	33948
0.1-0.2	14791
0.2-0.3	895
0.3-0.4	164
0.4-0.5	46
0.5-0.6	11
0.6-0.7	1
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
0.8378	Intermediate Similarity	NPC607762
0.6375	Remote Similarity	NPC601188
0.5676	Remote Similarity	NPC139364
0.5588	Remote Similarity	NPC234560
0.5541	Remote Similarity	NPC12377
0.5479	Remote Similarity	NPC209560
0.5479	Remote Similarity	NPC490700
0.5467	Remote Similarity	NPC80710
0.5325	Remote Similarity	NPC35544
0.5211	Remote Similarity	NPC242893
0.5205	Remote Similarity	NPC487215
0.5205	Remote Similarity	NPC518201
0.5181	Remote Similarity	NPC605728

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC607477 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5703
0.1-0.2	3415
0.2-0.3	27
0.3-0.4	5
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