NPASS Compound

Natural Product: NPC472648

Natural Product ID	NPC472648
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	NCJFUMIYGKGKEA-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3581374
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000025] Phenanthrenes and derivatives [CHEMONTID:0003007] Phenanthrols

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 63 68 0 0 0 0 0 0 0 0999 V2000 3.9957 -3.2131 -2.8546 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8088 -2.1420 -1.9893 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6603 -1.8500 -1.3089 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5706 -2.6931 -1.4889 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3727 -2.4714 -0.8403 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7104 -3.3320 -1.0360 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2509 -1.3878 0.0079 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3208 -0.5444 0.1963 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5167 -0.7799 -0.4618 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5538 0.1116 -0.2247 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7658 -0.0511 -0.8354 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8061 0.8632 -0.5828 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6449 1.9233 0.2639 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4243 2.0786 0.8727 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3640 1.1928 0.6491 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1627 1.4011 1.2893 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1495 0.5160 1.0473 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6373 2.8405 0.5381 O 0 0 0 0 0 0 0 0 0 0 0 0 7.9311 2.7721 -0.0361 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0311 -1.1904 0.6732 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2945 -1.7572 1.8987 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3061 -2.5343 2.5054 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5008 -1.5704 2.5234 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5225 -0.7916 1.9435 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2798 -0.2196 0.7279 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0484 -0.4258 0.1113 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7898 0.0887 -1.2369 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5573 1.2928 -1.5953 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9220 1.3243 -1.0437 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2660 0.6820 0.1304 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5277 0.8031 0.6710 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4633 1.5855 0.0132 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1408 2.2364 -1.1679 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8875 2.1108 -1.6941 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0664 3.0258 -1.8454 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7005 -0.6502 2.6296 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9468 -1.2353 3.8715 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0728 -3.3610 -3.0769 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4678 -2.9963 -3.8114 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5502 -4.1378 -2.3935 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6119 -3.5559 -2.1418 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9662 -3.5452 -1.9980 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9535 -0.8505 -1.5008 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7366 0.6814 -1.0935 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2570 2.9040 1.5488 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0505 2.2574 1.9658 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1839 0.6595 1.5442 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5185 2.0565 0.5787 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9096 2.3500 -1.0710 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4426 3.7479 0.0077 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2202 -2.1361 3.2721 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7294 -2.0060 3.4836 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6852 0.2262 -1.4189 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1366 -0.7459 -1.9339 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6289 1.4183 -2.7141 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0274 2.2046 -1.1991 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8648 0.3403 1.5586 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4695 1.7253 0.3786 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5805 2.5885 -2.6018 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8251 2.6441 -2.3872 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7802 -2.3285 3.8907 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9872 -0.9603 4.1683 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2685 -0.7852 4.6233 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 1 0 5 7 2 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 13 18 1 0 18 19 1 0 7 20 1 0 20 21 2 0 21 22 1 0 21 23 1 0 23 24 2 0 24 25 1 0 25 26 2 0 26 27 1 0 27 28 1 0 28 29 1 0 29 30 2 0 30 31 1 0 31 32 2 0 32 33 1 0 33 34 2 0 33 35 1 0 24 36 1 0 36 37 1 0 9 3 1 0 15 10 1 0 26 20 1 0 34 29 1 0 17 8 1 0 30 25 1 0 1 38 1 0 1 39 1 0 1 40 1 0 4 41 1 0 6 42 1 0 11 43 1 0 12 44 1 0 14 45 1 0 16 46 1 0 17 47 1 0 19 48 1 0 19 49 1 0 19 50 1 0 22 51 1 0 23 52 1 0 27 53 1 0 27 54 1 0 28 55 1 0 28 56 1 0 31 57 1 0 32 58 1 0 34 59 1 0 35 60 1 0 37 61 1 0 37 62 1 0 37 63 1 0 M END

Standard InCHIKey	NCJFUMIYGKGKEA-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C31H26O6/c1-35-19-7-11-21-17(13-19)5-9-23-29(21)27(37-3)15-25(34)31(23)30-22-8-4-16-12-18(32)6-10-20(16)28(22)26(36-2)14-24(30)33/h5-7,9-15,32-34H,4,8H2,1-3H3
SMILES	COc1cc(O)c(c2c1c1ccc(cc1cc2)OC)c1c(O)cc(c2c1CCc1c2ccc(c1)O)OC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	494.17	Volume:	511.861 ? Van der Waals volume.
Dense:	0.965	LogP:	4.448 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.737 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-6.638 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	32.0
TPSA:	88.38 ? Topological Polar Surface Area.	H-Bond Acceptor:	6.0
H-Bond Donor:	3.0	Rings:	6.0
Heavy Atoms:	6.0

MedChem Properties

QED Drug-Likeness Score:	0.245	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.828	Fsp³:	0.161
MCE-18:	71.778 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	1.0	Fluc inhibitor:	0.565 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.561 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.923 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.284	Promiscuous compounds:	0.163

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.999	MDCK Permeability:	-4.787
Pgp-inhibitor:	0.027	Pgp-substrate:	0.25
PAMPA:	0.122 ? 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):	0.008
20% Bioavailability (F20%):	0.308	30% Bioavailability (F30%):	0.315
50% Bioavailability (F50%):	0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.007	MRP1:	0.914
Plasma Protein Binding (PPB):	98.257%	Volume Distribution (VD):	0.446
Fu:	0.938% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.989
OATP1B3 inhibitor:	0.999	BCRP inhibitor:	0.872
BSEP inhibitor:	0.975

ADMET: Metabolism

CYP1A2-inhibitor:	1.0	CYP1A2-substrate:	0.984
CYP2C19-inhibitor:	0.999	CYP2C19-substrate:	0.99
CYP2C9-inhibitor:	1.0	CYP2C9-substrate:	0.084
CYP2D6-inhibitor:	1.0	CYP2D6-substrate:	0.979
CYP3A4-inhibitor:	0.066	CYP3A4-substrate:	0.913
CYP2B6-substrate:	0.998	CYP2C8-inhibitor:	0.999
HLM stability:	1.0 ? 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):

3.88

Half-life (T1/2):

1.378

ADMET: Toxicity

hERG Blockers:	0.653	hERG Blockers (10um):	0.721
Human Hepatotoxicity (H-HT):	0.793	Drug-induced Liver Injury (DILI):	0.906
AMES Toxicity:	0.929	Rat Oral Acute Toxicity:	0.75
Maximum Recommended Daily Dose:	0.976	Skin Sensitization:	0.527
Carcinogencity:	0.922	Eye Corrosion:	0.0
Eye Irritation:	0.161	Respiratory Toxicity:	0.993
Drug-induced Neurotoxicity:	0.884	Ototoxicity:	0.873
Hematotoxicity:	0.6	Drug-induced Nephrotoxicity:	0.865
Genotoxicity:	0.907	RPMI-8226 Immunitoxicity:	0.273
A549 Cytotoxicity:	0.944	Hek293 Cytotoxicity:	0.953
BCF:	1.639 ? 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:	5.091 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.158 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.778 ? 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
NPO10780	Bletilla striata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15686910]
NPO10780	Bletilla striata	Species	Orchidaceae	Eukaryota	Fibrous Roots	n.a.	n.a.	PMID[25760525]
NPO10780	Bletilla striata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31415170]
NPO10780	Bletilla striata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10780	Bletilla striata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10780	Bletilla striata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10780	Bletilla striata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10780	Bletilla striata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO10780	Bletilla striata	Species	Orchidaceae	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
MIC	8

Activity Type	# Activity
Organism	8

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
NPT1204	Organism	Enterococcus faecalis ATCC 29212	Enterococcus faecalis ATCC 29212	MIC	=	4.0	ug.mL-1	PMID[17438047]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	=	4.0	ug.mL-1	PMID[12617583]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	2.0	ug.mL-1	PMID[19179074]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	4.0	ug.mL-1	PMID[16643039]
NPT17	Organism	Staphylococcus epidermidis	Staphylococcus epidermidis	MIC	=	4.0	ug.mL-1	PMID[14698179]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	128.0	ug.mL-1	PMID[20405847]
NPT766	Organism	Proteus vulgaris	Proteus vulgaris	MIC	>	128.0	ug.mL-1	PMID[24417566]

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 NPC472648 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	27402
0.1-0.2	21199
0.2-0.3	1182
0.3-0.4	44
0.4-0.5	15
0.5-0.6	10
0.6-0.7	3
0.7-0.8	0
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8169	Intermediate Similarity	NPC206525
0.8143	Intermediate Similarity	NPC472649
0.6364	Remote Similarity	NPC472646
0.6104	Remote Similarity	NPC472647
0.6061	Remote Similarity	NPC258780
0.5606	Remote Similarity	NPC71465
0.5588	Remote Similarity	NPC294436
0.5542	Remote Similarity	NPC220688
0.5541	Remote Similarity	NPC31342
0.5479	Remote Similarity	NPC478417
0.5432	Remote Similarity	NPC232525
0.5417	Remote Similarity	NPC170328
0.5405	Remote Similarity	NPC191462
0.5132	Remote Similarity	NPC273623
0.5065	Remote Similarity	NPC58963

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC472648 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5749
0.1-0.2	3384
0.2-0.3	17
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