NPASS Compound

Natural Product: NPC502879

Natural Product ID	NPC502879
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	1-Hydroxy-13-dihydrodaunomycin
IUPAC Name	(7~{R},9~{R})-7-[(2~{R},4~{S},5~{S},6~{S})-4-amino-5-hydroxy-6-methyl-tetrahydropyran-2-yl]oxy-1,6,9,11-tetrahydroxy-9-[(1~{S})-1-hydroxyethyl]-4-methoxy-8,10-dihydro-7~{H}-tetracene-5,12-dione
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
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 70 74 0 0 0 0 0 0 0 0999 V2000 3.8738 4.5238 3.8167 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3967 3.4650 3.0216 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2972 2.5748 2.4795 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6560 2.6862 2.6898 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5580 1.7936 2.1462 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1239 0.7560 1.3705 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9729 -0.1782 0.7922 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7649 0.6304 1.1500 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8600 1.5271 1.6964 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4281 1.4167 1.4799 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5836 2.1903 1.9450 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9697 0.2913 0.6400 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6257 0.1330 0.3977 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2399 1.0376 0.9551 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1599 -0.8848 -0.3675 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0585 -1.7766 -0.9102 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5092 -2.8772 -1.7271 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5826 -3.5279 -0.9036 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0728 -4.1178 0.2006 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1848 -4.6199 -1.7752 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.1362 -5.4925 -0.9633 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1776 -5.4676 -2.2339 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6017 -2.5943 -0.3619 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2972 -1.1180 -0.6771 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.0822 -0.2391 -0.0160 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9005 0.5423 -0.8153 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3693 0.2659 -0.5884 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1387 1.4111 -1.1627 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.8013 1.6215 -2.5506 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.8808 2.6320 -0.3074 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1608 3.8132 -1.0169 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4327 2.5780 0.1220 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9148 3.9510 0.4687 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6137 1.8997 -0.7533 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3912 -1.6414 -0.6854 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3455 -2.5107 -1.2073 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8649 -0.6006 0.0962 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2896 -0.4586 0.3343 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1076 -1.2918 -0.1756 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6754 5.0529 3.2797 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0147 5.1871 4.0329 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3170 4.1452 4.7598 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0287 3.5104 3.3088 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6175 1.9096 2.3307 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2405 -0.9671 1.3852 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5080 1.0959 1.9152 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0265 -2.4337 -2.6217 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2623 -3.6381 -1.9664 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8857 -4.5763 -0.0657 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6737 -4.1796 -2.6518 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9692 -4.8695 -0.6027 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4648 -6.3111 -1.6399 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5401 -5.9288 -0.1284 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2450 -5.9648 -1.4960 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7208 -2.6767 0.7466 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5874 -2.8348 -0.8204 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3812 -1.0784 -1.7878 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6921 0.2318 -1.8711 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6663 -0.6546 -1.1713 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6343 0.0685 0.4468 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2272 1.1715 -1.0332 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1281 0.7849 -3.0733 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2882 2.4444 -2.9426 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5527 2.6529 0.5831 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4720 3.8682 -1.7318 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4242 1.9931 1.0885 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4179 4.3658 1.3655 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8341 3.9923 0.5913 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1671 4.6461 -0.3722 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6410 -3.3510 -0.7286 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 2 0 6 7 1 0 6 8 1 0 8 9 2 0 9 10 1 0 10 11 2 0 10 12 1 0 12 13 2 0 13 14 1 0 13 15 1 0 15 16 2 0 16 17 1 0 17 18 1 0 18 19 1 1 18 20 1 0 20 21 1 0 20 22 1 0 18 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 28 30 1 0 30 31 1 0 30 32 1 0 32 33 1 0 32 34 1 0 16 35 1 0 35 36 1 0 35 37 2 0 37 38 1 0 38 39 2 0 9 3 1 0 37 12 1 0 38 8 1 0 24 15 1 0 34 26 1 0 1 40 1 0 1 41 1 0 1 42 1 0 4 43 1 0 5 44 1 0 7 45 1 0 14 46 1 0 17 47 1 0 17 48 1 0 19 49 1 0 20 50 1 6 21 51 1 0 21 52 1 0 21 53 1 0 22 54 1 0 23 55 1 0 23 56 1 0 24 57 1 6 26 58 1 6 27 59 1 0 27 60 1 0 28 61 1 6 29 62 1 0 29 63 1 0 30 64 1 1 31 65 1 0 32 66 1 1 33 67 1 0 33 68 1 0 33 69 1 0 36 70 1 0 M END

Standard InCHIKey	BYWXYBOMWRGTBD-QSUBXWHHSA-N
Standard InCHI	InChI=1S/C27H31NO11/c1-9-22(31)12(28)6-16(38-9)39-15-8-27(36,10(2)29)7-11-17(15)24(33)21-20(23(11)32)25(34)18-13(30)4-5-14(37-3)19(18)26(21)35/h4-5,9-10,12,15-16,22,29-33,36H,6-8,28H2,1-3H3/t9-,10-,12-,15+,16-,22+,27+/m0/s1
SMILES	COC1=CC=C(O)C2=C1C(=O)C1=C(O)C3=C(C[C@](O)([C@H](C)O)C[C@H]3O[C@H]3C[C@H](N)[C@H](O)[C@H](C)O3)C(O)=C1C2=O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	545.19	Volume:	519.363 ? Van der Waals volume.
Dense:	1.05	LogP:	1.409 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.927 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.432 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	29.0
TPSA:	209.23 ? Topological Polar Surface Area.	H-Bond Acceptor:	12.0
H-Bond Donor:	8.0	Rings:	5.0
Heavy Atoms:	12.0

MedChem Properties

QED Drug-Likeness Score:	0.224	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.724	Fsp³:	0.481
MCE-18:	124.2 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	1
Colloidal aggregators:	0.579	Fluc inhibitor:	0.011 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.378 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.644 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.014	Promiscuous compounds:	0.58

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.649	MDCK Permeability:	-5.391
Pgp-inhibitor:	0.0	Pgp-substrate:	0.996
PAMPA:	1.0 ? 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):	0.982
20% Bioavailability (F20%):	0.999	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.981
Plasma Protein Binding (PPB):	91.657%	Volume Distribution (VD):	1.376
Fu:	10.098% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.916
OATP1B3 inhibitor:	0.981	BCRP inhibitor:	0.044
BSEP inhibitor:	0.006

ADMET: Metabolism

CYP1A2-inhibitor:	0.007	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.001	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.006	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.834
HLM stability:	0.028 ? 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):

6.975

Half-life (T1/2):

3.742

ADMET: Toxicity

hERG Blockers:	0.085	hERG Blockers (10um):	0.282
Human Hepatotoxicity (H-HT):	0.99	Drug-induced Liver Injury (DILI):	0.998
AMES Toxicity:	0.997	Rat Oral Acute Toxicity:	0.956
Maximum Recommended Daily Dose:	0.986	Skin Sensitization:	1.0
Carcinogencity:	0.87	Eye Corrosion:	0.0
Eye Irritation:	0.03	Respiratory Toxicity:	0.99
Drug-induced Neurotoxicity:	0.746	Ototoxicity:	0.976
Hematotoxicity:	0.882	Drug-induced Nephrotoxicity:	0.997
Genotoxicity:	1.0	RPMI-8226 Immunitoxicity:	0.89
A549 Cytotoxicity:	1.0	Hek293 Cytotoxicity:	0.954
BCF:	0.658 ? 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:	3.397 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.89 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.145 ? 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
NPO57282	Streptomyces coeruleorubidus ME130-A4 mutant	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

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

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 NPC502879 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	12627
0.1-0.2	35541
0.2-0.3	1654
0.3-0.4	24
0.4-0.5	2
0.5-0.6	2
0.6-0.7	7
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
0.7407	Intermediate Similarity	NPC601855
0.725	Intermediate Similarity	NPC603200
0.6951	Remote Similarity	NPC109403
0.6867	Remote Similarity	NPC487573
0.6706	Remote Similarity	NPC261012
0.6706	Remote Similarity	NPC314738
0.6628	Remote Similarity	NPC468994
0.6543	Remote Similarity	NPC602774
0.6049	Remote Similarity	NPC611971
0.5275	Remote Similarity	NPC603758
0.5104	Remote Similarity	NPC600087

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC502879 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3904
0.1-0.2	5190
0.2-0.3	26
0.3-0.4	5
0.4-0.5	11
0.5-0.6	6
0.6-0.7	8
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
0.6951	Remote Similarity	NPD6778	Phase 4
0.6867	Remote Similarity	NPD6777	Approved
0.6706	Remote Similarity	NPD6781	Phase 4
0.6706	Remote Similarity	NPD6782	Phase 4
0.6628	Remote Similarity	NPD6779	Approved
0.6628	Remote Similarity	NPD6780	Approved
0.6064	Remote Similarity	NPD6776	Approved
0.6049	Remote Similarity	NPD6535	Phase 4
0.5976	Remote Similarity	NPD6534	Approved
0.5699	Remote Similarity	NPD6823	Phase 2
0.5278	Remote Similarity	NPD8058	Clinical (unspecified phase)
0.5278	Remote Similarity	NPD8059	Phase 3
0.5053	Remote Similarity	NPD7699	Phase 2
0.5053	Remote Similarity	NPD7700	Phase 2

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