Structure

Physi-Chem Properties

Molecular Weight:  462.13
Volume:  433.214
LogP:  2.282
LogD:  1.226
LogS:  -3.183
# Rotatable Bonds:  15
TPSA:  131.5
# H-Bond Aceptor:  10
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  11

MedChem Properties

QED Drug-Likeness Score:  0.253
Synthetic Accessibility Score:  4.449
Fsp3:  0.65
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.282
MDCK Permeability:  0.00012509040243458003
Pgp-inhibitor:  0.091
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.971
20% Bioavailability (F20%):  0.938
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.876
Plasma Protein Binding (PPB):  44.84457015991211%
Volume Distribution (VD):  1.06
Pgp-substrate:  32.54136276245117%

ADMET: Metabolism

CYP1A2-inhibitor:  0.272
CYP1A2-substrate:  0.019
CYP2C19-inhibitor:  0.028
CYP2C19-substrate:  0.059
CYP2C9-inhibitor:  0.025
CYP2C9-substrate:  0.029
CYP2D6-inhibitor:  0.962
CYP2D6-substrate:  0.046
CYP3A4-inhibitor:  0.421
CYP3A4-substrate:  0.16

ADMET: Excretion

Clearance (CL):  2.275
Half-life (T1/2):  0.949

ADMET: Toxicity

hERG Blockers:  0.129
Human Hepatotoxicity (H-HT):  0.936
Drug-inuced Liver Injury (DILI):  0.916
AMES Toxicity:  0.055
Rat Oral Acute Toxicity:  0.613
Maximum Recommended Daily Dose:  0.307
Skin Sensitization:  0.936
Carcinogencity:  0.08
Eye Corrosion:  0.857
Eye Irritation:  0.046
Respiratory Toxicity:  0.964

Download Data

Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC473947

Natural Product ID:  NPC473947
Common Name*:   [(1S,2R,3S)-1,2-Diacetyloxy-1-[(2R,3S)-3-Acetyloxy-6-Oxo-2,3-Dihydropyran-2-Yl]Heptan-3-Yl] 2-Chloroacetate
IUPAC Name:   [(1S,2R,3S)-1,2-diacetyloxy-1-[(2R,3S)-3-acetyloxy-6-oxo-2,3-dihydropyran-2-yl]heptan-3-yl] 2-chloroacetate
Synonyms:  
Standard InCHIKey:  KXDJKKOPESVDBF-OFDAHSHWSA-N
Standard InCHI:  InChI=1S/C20H27ClO10/c1-5-6-7-14(30-17(26)10-21)18(28-12(3)23)20(29-13(4)24)19-15(27-11(2)22)8-9-16(25)31-19/h8-9,14-15,18-20H,5-7,10H2,1-4H3/t14-,15-,18+,19+,20-/m0/s1
SMILES:  CCCCC(C(C(C1C(C=CC(=O)O1)OC(=O)C)OC(=O)C)OC(=O)C)OC(=O)CCl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL455890
PubChem CID:   10412044
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0002995] Pentacarboxylic acids and derivatives

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO28865 Hyptis pectinata Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[8496706]
NPO28865 Hyptis pectinata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28865 Hyptis pectinata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[Title]
NPO28865 Hyptis pectinata Species Lamiaceae 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 NP ID 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT79 Organism Bacillus subtilis Bacillus subtilis IZ = 7.0 mm PMID[546041]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 5.0 mm PMID[546041]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 50.0 ug.mL-1 PMID[546041]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 75.0 ug.mL-1 PMID[546041]
NPT19 Organism Escherichia coli Escherichia coli MIC = 300.0 ug.mL-1 PMID[546041]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC = 300.0 ug.mL-1 PMID[546041]
NPT20 Organism Candida albicans Candida albicans MIC = 200.0 ug.mL-1 PMID[546041]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC473947 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.9041 High Similarity NPC475762
0.863 High Similarity NPC475760
0.8462 Intermediate Similarity NPC474026
0.825 Intermediate Similarity NPC180725
0.8148 Intermediate Similarity NPC133226
0.8148 Intermediate Similarity NPC470147
0.8125 Intermediate Similarity NPC248775
0.8082 Intermediate Similarity NPC25747
0.8082 Intermediate Similarity NPC148233
0.8025 Intermediate Similarity NPC470148
0.8025 Intermediate Similarity NPC470149
0.8 Intermediate Similarity NPC477428
0.7975 Intermediate Similarity NPC327041
0.7975 Intermediate Similarity NPC285840
0.7949 Intermediate Similarity NPC185186
0.7949 Intermediate Similarity NPC327383
0.7867 Intermediate Similarity NPC124586
0.7778 Intermediate Similarity NPC475711
0.7671 Intermediate Similarity NPC26223
0.76 Intermediate Similarity NPC308457
0.7534 Intermediate Similarity NPC22897
0.7534 Intermediate Similarity NPC159650
0.7531 Intermediate Similarity NPC477421
0.75 Intermediate Similarity NPC329914
0.7412 Intermediate Similarity NPC469469
0.7386 Intermediate Similarity NPC208473
0.7381 Intermediate Similarity NPC139712
0.7381 Intermediate Similarity NPC1180
0.7349 Intermediate Similarity NPC233071
0.7284 Intermediate Similarity NPC329890
0.7253 Intermediate Similarity NPC177668
0.725 Intermediate Similarity NPC476012
0.7229 Intermediate Similarity NPC188860
0.7159 Intermediate Similarity NPC473308
0.7143 Intermediate Similarity NPC133450
0.7126 Intermediate Similarity NPC251026
0.7065 Intermediate Similarity NPC3952
0.7051 Intermediate Similarity NPC96414
0.7045 Intermediate Similarity NPC473315
0.7045 Intermediate Similarity NPC142111
0.7037 Intermediate Similarity NPC476037
0.7037 Intermediate Similarity NPC477429
0.7037 Intermediate Similarity NPC323677
0.7021 Intermediate Similarity NPC256368
0.7011 Intermediate Similarity NPC8538
0.7011 Intermediate Similarity NPC184208
0.6988 Remote Similarity NPC477204
0.6966 Remote Similarity NPC474251
0.6962 Remote Similarity NPC201356
0.6889 Remote Similarity NPC470124
0.6882 Remote Similarity NPC473311
0.686 Remote Similarity NPC477314
0.686 Remote Similarity NPC28049
0.6854 Remote Similarity NPC170286
0.6848 Remote Similarity NPC233551
0.6848 Remote Similarity NPC40376
0.6848 Remote Similarity NPC21208
0.6848 Remote Similarity NPC20339
0.6848 Remote Similarity NPC48338
0.6848 Remote Similarity NPC280621
0.6842 Remote Similarity NPC474267
0.6835 Remote Similarity NPC19769
0.6824 Remote Similarity NPC326661
0.6818 Remote Similarity NPC471552
0.6818 Remote Similarity NPC315731
0.6818 Remote Similarity NPC473339
0.6813 Remote Similarity NPC204048
0.6813 Remote Similarity NPC47937
0.6804 Remote Similarity NPC475332
0.6782 Remote Similarity NPC477088
0.6778 Remote Similarity NPC160517
0.6778 Remote Similarity NPC78673
0.6778 Remote Similarity NPC186155
0.6753 Remote Similarity NPC158368
0.6753 Remote Similarity NPC154908
0.6753 Remote Similarity NPC226872
0.6753 Remote Similarity NPC252851
0.675 Remote Similarity NPC276299
0.675 Remote Similarity NPC248125
0.675 Remote Similarity NPC284447
0.6744 Remote Similarity NPC477203
0.6742 Remote Similarity NPC10080
0.6742 Remote Similarity NPC123908
0.6739 Remote Similarity NPC178215
0.6737 Remote Similarity NPC472196
0.6737 Remote Similarity NPC472195
0.6737 Remote Similarity NPC238090
0.6711 Remote Similarity NPC23418
0.6709 Remote Similarity NPC477456
0.6709 Remote Similarity NPC477457
0.6707 Remote Similarity NPC151481
0.6705 Remote Similarity NPC121374
0.6705 Remote Similarity NPC474739
0.6703 Remote Similarity NPC471494
0.6703 Remote Similarity NPC322529
0.6703 Remote Similarity NPC182383
0.6703 Remote Similarity NPC477014
0.6703 Remote Similarity NPC120398
0.6703 Remote Similarity NPC477013
0.6703 Remote Similarity NPC329615
0.6703 Remote Similarity NPC471567
0.6703 Remote Similarity NPC329838
0.6702 Remote Similarity NPC471569
0.6702 Remote Similarity NPC239517
0.6701 Remote Similarity NPC173329
0.6701 Remote Similarity NPC288350
0.6667 Remote Similarity NPC26810
0.6667 Remote Similarity NPC44261
0.6667 Remote Similarity NPC89001
0.6667 Remote Similarity NPC320458
0.6667 Remote Similarity NPC159698
0.6667 Remote Similarity NPC470137
0.6667 Remote Similarity NPC473905
0.6633 Remote Similarity NPC245521
0.6632 Remote Similarity NPC114172
0.6632 Remote Similarity NPC476075
0.6632 Remote Similarity NPC469410
0.6632 Remote Similarity NPC471324
0.6632 Remote Similarity NPC206679
0.6632 Remote Similarity NPC476084
0.663 Remote Similarity NPC114694
0.663 Remote Similarity NPC61527
0.663 Remote Similarity NPC62118
0.663 Remote Similarity NPC107717
0.663 Remote Similarity NPC311163
0.663 Remote Similarity NPC142117
0.663 Remote Similarity NPC240695
0.663 Remote Similarity NPC279267
0.663 Remote Similarity NPC103523
0.663 Remote Similarity NPC171174
0.663 Remote Similarity NPC475581
0.663 Remote Similarity NPC477015
0.663 Remote Similarity NPC231096
0.663 Remote Similarity NPC134865
0.663 Remote Similarity NPC69082
0.663 Remote Similarity NPC232555
0.6629 Remote Similarity NPC297440
0.6628 Remote Similarity NPC469880
0.6628 Remote Similarity NPC477202
0.6627 Remote Similarity NPC469660
0.6596 Remote Similarity NPC473504
0.6596 Remote Similarity NPC42598
0.6596 Remote Similarity NPC40066
0.6596 Remote Similarity NPC477017
0.6596 Remote Similarity NPC477011
0.6596 Remote Similarity NPC91067
0.6596 Remote Similarity NPC318963
0.6596 Remote Similarity NPC81778
0.6596 Remote Similarity NPC20621
0.6596 Remote Similarity NPC93794
0.6596 Remote Similarity NPC477016
0.6593 Remote Similarity NPC163093
0.6593 Remote Similarity NPC475035
0.6593 Remote Similarity NPC156804
0.6593 Remote Similarity NPC30915
0.6593 Remote Similarity NPC266718
0.6591 Remote Similarity NPC226226
0.6591 Remote Similarity NPC55304
0.6585 Remote Similarity NPC218477
0.6562 Remote Similarity NPC109406
0.6562 Remote Similarity NPC159092
0.6559 Remote Similarity NPC258068
0.6559 Remote Similarity NPC475037
0.6559 Remote Similarity NPC20533
0.6559 Remote Similarity NPC199382
0.6559 Remote Similarity NPC476583
0.6556 Remote Similarity NPC475690
0.6548 Remote Similarity NPC477084
0.6543 Remote Similarity NPC146811
0.6531 Remote Similarity NPC472995
0.6531 Remote Similarity NPC255410
0.6526 Remote Similarity NPC475748
0.6526 Remote Similarity NPC473904
0.6522 Remote Similarity NPC82795
0.6522 Remote Similarity NPC473478
0.6522 Remote Similarity NPC473669
0.6522 Remote Similarity NPC66346
0.6522 Remote Similarity NPC475034
0.6522 Remote Similarity NPC473651
0.6522 Remote Similarity NPC110710
0.6522 Remote Similarity NPC231009
0.6522 Remote Similarity NPC223871
0.6522 Remote Similarity NPC107986
0.6522 Remote Similarity NPC103284
0.6522 Remote Similarity NPC1083
0.6522 Remote Similarity NPC132496
0.6522 Remote Similarity NPC283085
0.6522 Remote Similarity NPC286338
0.65 Remote Similarity NPC98813
0.65 Remote Similarity NPC13743
0.6489 Remote Similarity NPC39754
0.6489 Remote Similarity NPC169511
0.6489 Remote Similarity NPC133730
0.6489 Remote Similarity NPC234077
0.6489 Remote Similarity NPC261952
0.6489 Remote Similarity NPC172821
0.6489 Remote Similarity NPC61257
0.6489 Remote Similarity NPC81045
0.6489 Remote Similarity NPC320569
0.6489 Remote Similarity NPC242364

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC473947 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.6882 Remote Similarity NPD7838 Discovery
0.6702 Remote Similarity NPD46 Approved
0.6702 Remote Similarity NPD6698 Approved
0.64 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6337 Remote Similarity NPD6648 Approved
0.6275 Remote Similarity NPD5344 Discontinued
0.622 Remote Similarity NPD2685 Clinical (unspecified phase)
0.604 Remote Similarity NPD4792 Clinical (unspecified phase)
0.6 Remote Similarity NPD1733 Clinical (unspecified phase)
0.596 Remote Similarity NPD7983 Approved
0.5833 Remote Similarity NPD7899 Clinical (unspecified phase)
0.578 Remote Similarity NPD6686 Approved
0.5773 Remote Similarity NPD4249 Approved
0.5729 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5714 Remote Similarity NPD4251 Approved
0.5714 Remote Similarity NPD4250 Approved
0.5684 Remote Similarity NPD5209 Approved
0.5638 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5625 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5619 Remote Similarity NPD4225 Approved
0.5607 Remote Similarity NPD3653 Clinical (unspecified phase)
0.56 Remote Similarity NPD1695 Approved

  Bioactivity similarity: Similar Natural Products in NPASS

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