Structure

Physi-Chem Properties

Molecular Weight:  382.13
Volume:  366.065
LogP:  1.064
LogD:  0.868
LogS:  -2.482
# Rotatable Bonds:  10
TPSA:  117.73
# H-Bond Aceptor:  9
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.274
Synthetic Accessibility Score:  4.773
Fsp3:  0.556
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.982
MDCK Permeability:  0.00011716510925907642
Pgp-inhibitor:  0.928
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.956
20% Bioavailability (F20%):  0.7
30% Bioavailability (F30%):  0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.712
Plasma Protein Binding (PPB):  72.31751251220703%
Volume Distribution (VD):  0.823
Pgp-substrate:  32.98604202270508%

ADMET: Metabolism

CYP1A2-inhibitor:  0.037
CYP1A2-substrate:  0.024
CYP2C19-inhibitor:  0.025
CYP2C19-substrate:  0.065
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.041
CYP2D6-inhibitor:  0.435
CYP2D6-substrate:  0.104
CYP3A4-inhibitor:  0.133
CYP3A4-substrate:  0.225

ADMET: Excretion

Clearance (CL):  2.084
Half-life (T1/2):  0.779

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.711
Drug-inuced Liver Injury (DILI):  0.81
AMES Toxicity:  0.07
Rat Oral Acute Toxicity:  0.604
Maximum Recommended Daily Dose:  0.832
Skin Sensitization:  0.873
Carcinogencity:  0.121
Eye Corrosion:  0.979
Eye Irritation:  0.551
Respiratory Toxicity:  0.522

Download Data

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

  Natural Product: NPC124586

Natural Product ID:  NPC124586
Common Name*:   10-Epi-Olguine
IUPAC Name:   [(2R,3S)-2-[(2S,3S)-3-[(E,3R,4S)-3,4-diacetyloxypent-1-enyl]oxiran-2-yl]-6-oxo-2,3-dihydropyran-3-yl] acetate
Synonyms:   10-Epi-Olguine
Standard InCHIKey:  WSMOXQBLJXEQNX-GMHYHFCSSA-N
Standard InCHI:  InChI=1S/C18H22O9/c1-9(23-10(2)19)13(24-11(3)20)5-6-15-17(26-15)18-14(25-12(4)21)7-8-16(22)27-18/h5-9,13-15,17-18H,1-4H3/b6-5+/t9-,13+,14-,15-,17-,18+/m0/s1
SMILES:  C[C@@H]([C@@H](/C=C/[C@H]1[C@@H]([C@H]2[C@H](C=CC(=O)O2)OC(=O)C)O1)OC(=O)C)OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL463301
PubChem CID:   6442294
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0002966] Tetracarboxylic 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
NPO27434 Rabdosia ternifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[9182128]
NPO27434 Rabdosia ternifolia 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
NPT1034 Cell Line Lu1 Homo sapiens ED50 = 4.8 ug ml-1 PMID[480996]
NPT1851 Cell Line Col2 Homo sapiens ED50 = 2.1 ug ml-1 PMID[480996]
NPT91 Cell Line KB Homo sapiens ED50 = 1.8 ug ml-1 PMID[480996]
NPT858 Cell Line LNCaP Homo sapiens ED50 = 1.2 ug ml-1 PMID[480996]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. ED50 = 1.8 ug ml-1 PMID[480996]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. ED50 = 2.1 ug ml-1 PMID[480996]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. ED50 = 2.2 ug ml-1 PMID[480996]

☑ 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 NPC124586 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
0.9672 High Similarity NPC148233
0.9672 High Similarity NPC308457
0.9672 High Similarity NPC25747
0.918 High Similarity NPC26223
0.9077 High Similarity NPC475760
0.8676 High Similarity NPC475762
0.8333 Intermediate Similarity NPC96414
0.8209 Intermediate Similarity NPC201356
0.8125 Intermediate Similarity NPC22897
0.8125 Intermediate Similarity NPC159650
0.8082 Intermediate Similarity NPC474026
0.806 Intermediate Similarity NPC19769
0.7941 Intermediate Similarity NPC276299
0.791 Intermediate Similarity NPC470808
0.7879 Intermediate Similarity NPC26810
0.7867 Intermediate Similarity NPC473947
0.7867 Intermediate Similarity NPC180725
0.7763 Intermediate Similarity NPC470147
0.7763 Intermediate Similarity NPC133226
0.7733 Intermediate Similarity NPC248775
0.7681 Intermediate Similarity NPC146811
0.7632 Intermediate Similarity NPC470149
0.7632 Intermediate Similarity NPC470148
0.7606 Intermediate Similarity NPC151481
0.7576 Intermediate Similarity NPC478095
0.7568 Intermediate Similarity NPC285840
0.7568 Intermediate Similarity NPC327041
0.7541 Intermediate Similarity NPC275316
0.7534 Intermediate Similarity NPC327383
0.7534 Intermediate Similarity NPC185186
0.7534 Intermediate Similarity NPC284006
0.75 Intermediate Similarity NPC318481
0.7468 Intermediate Similarity NPC315559
0.7465 Intermediate Similarity NPC63873
0.7432 Intermediate Similarity NPC107654
0.7429 Intermediate Similarity NPC248125
0.7424 Intermediate Similarity NPC478096
0.7403 Intermediate Similarity NPC271632
0.7397 Intermediate Similarity NPC293114
0.7368 Intermediate Similarity NPC233071
0.7368 Intermediate Similarity NPC475711
0.7361 Intermediate Similarity NPC475982
0.7342 Intermediate Similarity NPC313677
0.7342 Intermediate Similarity NPC251026
0.7324 Intermediate Similarity NPC122627
0.7324 Intermediate Similarity NPC203335
0.7313 Intermediate Similarity NPC302564
0.7286 Intermediate Similarity NPC273600
0.726 Intermediate Similarity NPC476037
0.726 Intermediate Similarity NPC476012
0.726 Intermediate Similarity NPC202011
0.725 Intermediate Similarity NPC44261
0.725 Intermediate Similarity NPC142111
0.725 Intermediate Similarity NPC473315
0.7246 Intermediate Similarity NPC217940
0.7246 Intermediate Similarity NPC474774
0.7237 Intermediate Similarity NPC188860
0.7215 Intermediate Similarity NPC469469
0.7206 Intermediate Similarity NPC79756
0.72 Intermediate Similarity NPC315843
0.72 Intermediate Similarity NPC473489
0.7183 Intermediate Similarity NPC475555
0.7183 Intermediate Similarity NPC475675
0.7179 Intermediate Similarity NPC1180
0.7162 Intermediate Similarity NPC316185
0.716 Intermediate Similarity NPC473308
0.7123 Intermediate Similarity NPC88877
0.7123 Intermediate Similarity NPC476591
0.7121 Intermediate Similarity NPC86948
0.7121 Intermediate Similarity NPC245002
0.7105 Intermediate Similarity NPC473582
0.7101 Intermediate Similarity NPC151648
0.7101 Intermediate Similarity NPC15193
0.7083 Intermediate Similarity NPC478100
0.7073 Intermediate Similarity NPC470124
0.7067 Intermediate Similarity NPC329890
0.7067 Intermediate Similarity NPC329914
0.7059 Intermediate Similarity NPC474267
0.7059 Intermediate Similarity NPC97570
0.7059 Intermediate Similarity NPC3952
0.7051 Intermediate Similarity NPC477314
0.7042 Intermediate Similarity NPC182794
0.7042 Intermediate Similarity NPC282760
0.7042 Intermediate Similarity NPC470123
0.7015 Intermediate Similarity NPC294938
0.7013 Intermediate Similarity NPC301525
0.7 Intermediate Similarity NPC44343
0.7 Intermediate Similarity NPC297440
0.7 Intermediate Similarity NPC179087
0.7 Intermediate Similarity NPC210303
0.6988 Remote Similarity NPC208473
0.6986 Remote Similarity NPC238223
0.6974 Remote Similarity NPC326504
0.697 Remote Similarity NPC474913
0.6962 Remote Similarity NPC139712
0.6944 Remote Similarity NPC284447
0.6944 Remote Similarity NPC478101
0.6901 Remote Similarity NPC475221
0.6901 Remote Similarity NPC477457
0.6901 Remote Similarity NPC477456
0.6883 Remote Similarity NPC473948
0.6867 Remote Similarity NPC475034
0.6866 Remote Similarity NPC327388
0.686 Remote Similarity NPC177668
0.6849 Remote Similarity NPC478097
0.6849 Remote Similarity NPC194871
0.6849 Remote Similarity NPC132286
0.6842 Remote Similarity NPC222244
0.6842 Remote Similarity NPC16349
0.6835 Remote Similarity NPC182292
0.6824 Remote Similarity NPC470137
0.6818 Remote Similarity NPC159535
0.6818 Remote Similarity NPC151761
0.6812 Remote Similarity NPC286189
0.6806 Remote Similarity NPC478099
0.6806 Remote Similarity NPC478098
0.6806 Remote Similarity NPC476589
0.68 Remote Similarity NPC469660
0.6795 Remote Similarity NPC326661
0.6786 Remote Similarity NPC204048
0.6786 Remote Similarity NPC477428
0.6765 Remote Similarity NPC323597
0.6765 Remote Similarity NPC471277
0.6765 Remote Similarity NPC323498
0.6765 Remote Similarity NPC471279
0.6765 Remote Similarity NPC211752
0.6765 Remote Similarity NPC129150
0.6757 Remote Similarity NPC218477
0.6757 Remote Similarity NPC276290
0.6757 Remote Similarity NPC470256
0.6753 Remote Similarity NPC474280
0.6753 Remote Similarity NPC474545
0.675 Remote Similarity NPC473981
0.675 Remote Similarity NPC471537
0.675 Remote Similarity NPC473980
0.6747 Remote Similarity NPC266718
0.6747 Remote Similarity NPC186155
0.6747 Remote Similarity NPC160517
0.6747 Remote Similarity NPC475035
0.6747 Remote Similarity NPC78673
0.6744 Remote Similarity NPC133450
0.6719 Remote Similarity NPC236338
0.6719 Remote Similarity NPC15789
0.6714 Remote Similarity NPC321919
0.6714 Remote Similarity NPC81896
0.6712 Remote Similarity NPC37382
0.6709 Remote Similarity NPC474278
0.6709 Remote Similarity NPC97516
0.6707 Remote Similarity NPC475046
0.6707 Remote Similarity NPC474959
0.6707 Remote Similarity NPC11383
0.6707 Remote Similarity NPC310450
0.6707 Remote Similarity NPC475690
0.6706 Remote Similarity NPC475037
0.6667 Remote Similarity NPC254095
0.6667 Remote Similarity NPC260396
0.6667 Remote Similarity NPC474084
0.6667 Remote Similarity NPC223679
0.6667 Remote Similarity NPC473311
0.6667 Remote Similarity NPC474739
0.6667 Remote Similarity NPC114464
0.6629 Remote Similarity NPC256368
0.6628 Remote Similarity NPC287089
0.6627 Remote Similarity NPC286770
0.6627 Remote Similarity NPC284472
0.6627 Remote Similarity NPC229799
0.6625 Remote Similarity NPC473471
0.6625 Remote Similarity NPC475699
0.6625 Remote Similarity NPC28049
0.6625 Remote Similarity NPC279532
0.6623 Remote Similarity NPC477303
0.6623 Remote Similarity NPC477311
0.6623 Remote Similarity NPC474705
0.6622 Remote Similarity NPC225272
0.6622 Remote Similarity NPC25298
0.662 Remote Similarity NPC55376
0.6618 Remote Similarity NPC472808
0.6618 Remote Similarity NPC324224
0.6588 Remote Similarity NPC61527
0.6585 Remote Similarity NPC315731
0.6585 Remote Similarity NPC184208
0.6585 Remote Similarity NPC141810
0.6585 Remote Similarity NPC474894
0.6585 Remote Similarity NPC8538
0.6582 Remote Similarity NPC203277
0.6582 Remote Similarity NPC301207
0.6582 Remote Similarity NPC470705
0.6582 Remote Similarity NPC209113
0.6582 Remote Similarity NPC127118
0.6582 Remote Similarity NPC190400
0.6582 Remote Similarity NPC49392
0.6579 Remote Similarity NPC59558
0.6579 Remote Similarity NPC329904
0.6579 Remote Similarity NPC473361
0.6575 Remote Similarity NPC471566
0.6575 Remote Similarity NPC471556
0.6575 Remote Similarity NPC471565
0.6571 Remote Similarity NPC82465
0.6571 Remote Similarity NPC222852
0.6567 Remote Similarity NPC478120

  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 NPC124586 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
0.7042 Intermediate Similarity NPD2685 Clinical (unspecified phase)
0.686 Remote Similarity NPD7838 Discovery
0.6667 Remote Similarity NPD46 Approved
0.6667 Remote Similarity NPD585 Clinical (unspecified phase)
0.6667 Remote Similarity NPD6698 Approved
0.6364 Remote Similarity NPD6927 Phase 3
0.6277 Remote Similarity NPD6648 Approved
0.6211 Remote Similarity NPD5344 Discontinued
0.6197 Remote Similarity NPD69 Approved
0.6197 Remote Similarity NPD6109 Phase 1
0.6197 Remote Similarity NPD9119 Approved
0.6163 Remote Similarity NPD6400 Clinical (unspecified phase)
0.6154 Remote Similarity NPD5343 Approved
0.6118 Remote Similarity NPD5209 Approved
0.6056 Remote Similarity NPD9118 Approved
0.6 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5938 Remote Similarity NPD6096 Approved
0.5938 Remote Similarity NPD6097 Approved
0.5909 Remote Similarity NPD1733 Clinical (unspecified phase)
0.5811 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5789 Remote Similarity NPD5325 Clinical (unspecified phase)
0.5769 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5698 Remote Similarity NPD5790 Clinical (unspecified phase)
0.567 Remote Similarity NPD4225 Approved
0.5606 Remote Similarity NPD3174 Discontinued

  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