NPASS Compound

Natural Product: NPC475933

Natural Product ID	NPC475933
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	NUUYNQBWBWOTRO-VTJPJHEDSA-N
IUPAC Name	n.a.
Synonyms	Celafolin B-2
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL518833
PubChem CID	44584404
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids [CHEMONTID:0002051] Agarofurans

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 66 69 0 0 0 0 0 0 0 0999 V2000 -4.4581 -0.8331 -0.7832 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5557 -0.4327 0.4020 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5556 1.0405 0.4592 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2692 1.7189 0.1071 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1143 1.0300 0.7826 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0259 -0.3587 0.2403 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2885 -1.1565 0.2997 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2007 -2.1684 1.4543 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2215 -3.1386 0.8734 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1482 -2.5275 0.7452 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0614 -1.0607 1.0487 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3470 -0.5084 0.7306 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1008 0.1679 1.6685 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6409 0.2963 2.8220 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4267 0.7505 1.3824 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9194 0.6276 0.1936 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2029 1.1631 -0.1744 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9950 1.8376 0.6949 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2274 2.3277 0.2654 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6524 2.1431 -1.0096 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8463 1.4610 -1.8807 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6377 0.9755 -1.4748 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8069 -3.2086 -0.5397 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2694 -1.9723 -0.8530 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8105 -3.7739 -1.5250 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9302 -4.2512 -0.4384 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4925 -0.2668 -1.1924 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0496 1.7082 0.4089 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2842 3.0586 0.5726 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1800 4.1512 -0.3025 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0731 3.8643 -1.5202 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1959 5.5559 0.1881 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2545 -0.0472 -0.8783 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9780 -1.7861 -0.5575 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8796 -0.8613 -1.7142 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1633 -0.7904 1.2911 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3386 1.5088 -0.2055 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8364 1.4283 1.4859 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1668 1.7623 -0.9869 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2442 1.0942 1.8626 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1999 -2.6502 1.5221 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9366 -1.7200 2.3934 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2347 -4.1219 1.3477 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8811 -2.9646 1.4417 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5556 -2.6309 -0.2774 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1294 -0.8294 2.0963 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9643 1.2664 2.1582 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3153 0.0893 -0.5461 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6833 1.9993 1.7139 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8186 2.8568 0.9961 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6068 2.5082 -1.3882 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1542 1.2895 -2.9244 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9833 0.4292 -2.1581 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3344 -4.4334 -2.2572 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2732 -3.0185 -2.0996 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1175 -4.4264 -0.9704 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1265 -4.7308 -1.4097 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6133 -5.0728 0.2678 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8466 -3.8296 -0.0106 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2756 0.7592 -1.4936 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2714 -0.6564 -1.9102 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4329 -0.8579 -1.3302 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1444 2.5865 0.0058 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6506 5.5984 1.1978 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7648 6.1455 -0.5619 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1389 5.8860 0.2539 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 2 0 13 15 1 0 15 16 2 3 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 20 21 1 0 21 22 2 0 9 23 1 0 23 24 1 0 23 25 1 0 23 26 1 0 6 27 1 0 5 28 1 0 4 29 1 0 29 30 1 0 30 31 2 0 30 32 1 0 7 2 1 0 11 6 1 0 24 7 1 0 22 17 1 0 1 33 1 0 1 34 1 0 1 35 1 0 2 36 1 0 3 37 1 0 3 38 1 0 4 39 1 0 5 40 1 0 8 41 1 0 8 42 1 0 9 43 1 0 10 44 1 0 10 45 1 0 11 46 1 0 15 47 1 0 16 48 1 0 18 49 1 0 19 50 1 0 20 51 1 0 21 52 1 0 22 53 1 0 25 54 1 0 25 55 1 0 25 56 1 0 26 57 1 0 26 58 1 0 26 59 1 0 27 60 1 0 27 61 1 0 27 62 1 0 28 63 1 0 32 64 1 0 32 65 1 0 32 66 1 0 M END

Standard InCHIKey	NUUYNQBWBWOTRO-VTJPJHEDSA-N
Standard InCHI	InChI=1S/C26H34O6/c1-16-13-20(30-17(2)27)23(29)25(5)21(14-19-15-26(16,25)32-24(19,3)4)31-22(28)12-11-18-9-7-6-8-10-18/h6-12,16,19-21,23,29H,13-15H2,1-5H3/b12-11+/t16-,19-,20+,21+,23+,25-,26+/m1/s1
SMILES	CC1CC(C(C2(C13CC(CC2OC(=O)C=CC4=CC=CC=C4)C(O3)(C)C)C)O)OC(=O)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	442.24	Volume:	460.949 ? Van der Waals volume.
Dense:	0.959	LogP:	3.639 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.41 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.772 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	23.0
TPSA:	82.06 ? Topological Polar Surface Area.	H-Bond Acceptor:	6.0
H-Bond Donor:	1.0	Rings:	4.0
Heavy Atoms:	6.0

MedChem Properties

QED Drug-Likeness Score:	0.562	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.667	Fsp³:	0.615
MCE-18:	131.19 ? 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:	0.703	Fluc inhibitor:	0.492 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.032 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.578 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.109	Promiscuous compounds:	0.018

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.081	MDCK Permeability:	-4.669
Pgp-inhibitor:	0.654	Pgp-substrate:	0.127
PAMPA:	0.421 ? 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):	0.003
20% Bioavailability (F20%):	0.154	30% Bioavailability (F30%):	0.587
50% Bioavailability (F50%):	0.983

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.736	MRP1:	0.997
Plasma Protein Binding (PPB):	85.982%	Volume Distribution (VD):	0.234
Fu:	9.886% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.697
OATP1B3 inhibitor:	0.933	BCRP inhibitor:	0.014
BSEP inhibitor:	0.991

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.107
CYP2C19-inhibitor:	0.003	CYP2C19-substrate:	0.018
CYP2C9-inhibitor:	0.582	CYP2C9-substrate:	0.003
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.002
CYP3A4-inhibitor:	0.007	CYP3A4-substrate:	0.013
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.129 ? 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):

4.221

Half-life (T1/2):

1.176

ADMET: Toxicity

hERG Blockers:	0.139	hERG Blockers (10um):	0.628
Human Hepatotoxicity (H-HT):	0.393	Drug-induced Liver Injury (DILI):	0.334
AMES Toxicity:	0.517	Rat Oral Acute Toxicity:	0.278
Maximum Recommended Daily Dose:	0.7	Skin Sensitization:	0.987
Carcinogencity:	0.208	Eye Corrosion:	0.002
Eye Irritation:	0.218	Respiratory Toxicity:	0.171
Drug-induced Neurotoxicity:	0.791	Ototoxicity:	0.642
Hematotoxicity:	0.036	Drug-induced Nephrotoxicity:	0.269
Genotoxicity:	0.038	RPMI-8226 Immunitoxicity:	0.078
A549 Cytotoxicity:	0.155	Hek293 Cytotoxicity:	0.592
BCF:	0.827 ? 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:	3.647 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.385 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.742 ? 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
NPO31542	Celastrus stephanotiifolius	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8350085]
NPO31542	Celastrus stephanotiifolius	Species	Celastraceae	Eukaryota	n.a.	seed	n.a.	PMID[8350085]
NPO31542	Celastrus stephanotiifolius	Species	Celastraceae	Eukaryota	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
Activity	8

Activity Type	# Activity
Cell line	4
Others	4

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
NPT80	Cell line	Raji	Homo sapiens	Activity	=	70.0	%	PubChem BioAssay data set
NPT80	Cell line	Raji	Homo sapiens	Activity	>	80.0	%	DrugMatrix in vitro pharmacology data
NPT2	Others	Unspecified	n.a.	Activity	=	0.0	%	PMID[15711537]
NPT2	Others	Unspecified	n.a.	Activity	=	41.6	%	PMID[12027764]
NPT2	Others	Unspecified	n.a.	Activity	=	86.4	%	PMID[6747989]
NPT2	Others	Unspecified	n.a.	Activity	=	100.0	%	PMID[9191970]

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 NPC475933 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	8015
0.1-0.2	36222
0.2-0.3	5251
0.3-0.4	285
0.4-0.5	69
0.5-0.6	10
0.6-0.7	4
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
0.7846	Intermediate Similarity	NPC473870
0.6522	Remote Similarity	NPC37641
0.6522	Remote Similarity	NPC114927
0.6377	Remote Similarity	NPC84129
0.6081	Remote Similarity	NPC473110
0.5921	Remote Similarity	NPC473082
0.5921	Remote Similarity	NPC214550
0.5769	Remote Similarity	NPC473083
0.5556	Remote Similarity	NPC473109
0.5301	Remote Similarity	NPC469349
0.5244	Remote Similarity	NPC483878
0.52	Remote Similarity	NPC473860
0.5181	Remote Similarity	NPC25768
0.5132	Remote Similarity	NPC470158
0.5067	Remote Similarity	NPC473869

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC475933 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3274
0.1-0.2	5676
0.2-0.3	197
0.3-0.4	3
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