Structure

Physi-Chem Properties

Molecular Weight:  318.15
Volume:  304.787
LogP:  -0.609
LogD:  -0.131
LogS:  -1.204
# Rotatable Bonds:  2
TPSA:  83.83
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.761
Synthetic Accessibility Score:  5.713
Fsp3:  1.0
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:  -4.813
MDCK Permeability:  1.4872966858092695e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.905
20% Bioavailability (F20%):  0.471
30% Bioavailability (F30%):  0.939

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.641
Plasma Protein Binding (PPB):  85.03141021728516%
Volume Distribution (VD):  1.262
Pgp-substrate:  18.750545501708984%

ADMET: Metabolism

CYP1A2-inhibitor:  0.009
CYP1A2-substrate:  0.94
CYP2C19-inhibitor:  0.01
CYP2C19-substrate:  0.894
CYP2C9-inhibitor:  0.012
CYP2C9-substrate:  0.068
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.13
CYP3A4-inhibitor:  0.026
CYP3A4-substrate:  0.405

ADMET: Excretion

Clearance (CL):  10.628
Half-life (T1/2):  0.19

ADMET: Toxicity

hERG Blockers:  0.03
Human Hepatotoxicity (H-HT):  0.507
Drug-inuced Liver Injury (DILI):  0.053
AMES Toxicity:  0.075
Rat Oral Acute Toxicity:  0.448
Maximum Recommended Daily Dose:  0.068
Skin Sensitization:  0.413
Carcinogencity:  0.921
Eye Corrosion:  0.589
Eye Irritation:  0.064
Respiratory Toxicity:  0.98

Download Data

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

  Natural Product: NPC470630

Natural Product ID:  NPC470630
Common Name*:   PBDNFCSOADCJKH-VYUINMPDSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  PBDNFCSOADCJKH-VYUINMPDSA-N
Standard InCHI:  InChI=1S/C15H26O5S/c1-9(2)15-8-7-13(3,20-15)10-5-6-14(4,21(17,18)19)11(10)12(15)16/h9-12,16H,5-8H2,1-4H3,(H,17,18,19)/t10?,11?,12-,13-,14-,15-/m0/s1
SMILES:  CC(C)C12CCC(O1)(C3CCC(C3C2O)(C)S(=O)(=O)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2112117
PubChem CID:   71461607
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

*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
NPO30648 Alisma orientale Species Alismataceae Eukaryota rhizome n.a. n.a. PMID[10560729]
NPO30648 Alisma orientale Species Alismataceae Eukaryota n.a. rhizome n.a. PMID[17541191]
NPO30648 Alisma orientale Species Alismataceae Eukaryota Rhizome n.a. n.a. PMID[26425784]
NPO30648 Alisma orientale Species Alismataceae Eukaryota n.a. tuber n.a. PMID[26666273]
NPO30648 Alisma orientale Species Alismataceae Eukaryota n.a. n.a. n.a. Database[HerDing]

☑ 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
NPT32 Organism Mus musculus Mus musculus Inhibition = 3.3 % PMID[531244]
NPT32 Organism Mus musculus Mus musculus Inhibition = -2.1 % PMID[531244]
NPT32 Organism Mus musculus Mus musculus Inhibition = 4.3 % PMID[531244]
NPT32 Organism Mus musculus Mus musculus Inhibition = 12.6 % PMID[531244]
NPT32 Organism Mus musculus Mus musculus Inhibition = 24.7 % PMID[531244]
NPT32 Organism Mus musculus Mus musculus IC50 > 100000.0 nM PMID[531244]

☑ 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 NPC470630 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
0.6933 Remote Similarity NPC476702
0.6933 Remote Similarity NPC199937
0.6875 Remote Similarity NPC248427
0.6757 Remote Similarity NPC475412
0.6747 Remote Similarity NPC64081
0.6747 Remote Similarity NPC474574
0.6667 Remote Similarity NPC470660
0.6667 Remote Similarity NPC470659
0.6627 Remote Similarity NPC279575
0.6627 Remote Similarity NPC470176
0.6591 Remote Similarity NPC320824
0.6588 Remote Similarity NPC81074
0.6588 Remote Similarity NPC477282
0.6575 Remote Similarity NPC119425
0.6548 Remote Similarity NPC133596
0.6548 Remote Similarity NPC188793
0.6548 Remote Similarity NPC11907
0.6506 Remote Similarity NPC231680
0.6506 Remote Similarity NPC91387
0.6506 Remote Similarity NPC270306
0.6447 Remote Similarity NPC172622
0.6429 Remote Similarity NPC470174
0.641 Remote Similarity NPC165069
0.64 Remote Similarity NPC185116
0.64 Remote Similarity NPC475968
0.6395 Remote Similarity NPC170595
0.6386 Remote Similarity NPC138273
0.6364 Remote Similarity NPC475388
0.6353 Remote Similarity NPC83108
0.6353 Remote Similarity NPC214030
0.6351 Remote Similarity NPC322148
0.6341 Remote Similarity NPC131506
0.6341 Remote Similarity NPC157777
0.6296 Remote Similarity NPC253123
0.6292 Remote Similarity NPC477285
0.6292 Remote Similarity NPC470070
0.6292 Remote Similarity NPC111582
0.625 Remote Similarity NPC216941
0.6234 Remote Similarity NPC475807
0.6203 Remote Similarity NPC472946
0.6203 Remote Similarity NPC250836
0.619 Remote Similarity NPC472945
0.619 Remote Similarity NPC472944
0.619 Remote Similarity NPC470151
0.618 Remote Similarity NPC311642
0.618 Remote Similarity NPC242771
0.618 Remote Similarity NPC475849
0.618 Remote Similarity NPC286719
0.618 Remote Similarity NPC164289
0.618 Remote Similarity NPC100366
0.618 Remote Similarity NPC477286
0.6145 Remote Similarity NPC470173
0.6136 Remote Similarity NPC66766
0.6136 Remote Similarity NPC117137
0.6118 Remote Similarity NPC472952
0.6118 Remote Similarity NPC472950
0.6118 Remote Similarity NPC131584
0.6118 Remote Similarity NPC139765
0.6111 Remote Similarity NPC217559
0.6111 Remote Similarity NPC292458
0.6111 Remote Similarity NPC474266
0.6111 Remote Similarity NPC268578
0.6092 Remote Similarity NPC469324
0.6087 Remote Similarity NPC215968
0.6087 Remote Similarity NPC155531
0.6082 Remote Similarity NPC469710
0.6067 Remote Similarity NPC190940
0.6067 Remote Similarity NPC473257
0.6064 Remote Similarity NPC82955
0.6061 Remote Similarity NPC473638
0.6061 Remote Similarity NPC473616
0.6049 Remote Similarity NPC179823
0.6047 Remote Similarity NPC293223
0.6047 Remote Similarity NPC473916
0.6047 Remote Similarity NPC477601
0.6047 Remote Similarity NPC477602
0.6047 Remote Similarity NPC136424
0.6044 Remote Similarity NPC474156
0.6044 Remote Similarity NPC227260
0.6023 Remote Similarity NPC31302
0.6023 Remote Similarity NPC245029
0.6022 Remote Similarity NPC161928
0.6022 Remote Similarity NPC472396
0.6022 Remote Similarity NPC210658
0.6 Remote Similarity NPC470262
0.6 Remote Similarity NPC102156
0.6 Remote Similarity NPC470611
0.6 Remote Similarity NPC166250
0.6 Remote Similarity NPC215030
0.6 Remote Similarity NPC148740
0.5979 Remote Similarity NPC473503
0.5978 Remote Similarity NPC232044
0.5978 Remote Similarity NPC290612
0.5978 Remote Similarity NPC273290
0.5957 Remote Similarity NPC128475
0.5955 Remote Similarity NPC16449
0.5952 Remote Similarity NPC157422
0.5952 Remote Similarity NPC8004
0.5952 Remote Similarity NPC127283
0.5952 Remote Similarity NPC252182
0.5952 Remote Similarity NPC109457
0.5952 Remote Similarity NPC100586
0.5952 Remote Similarity NPC470071
0.5952 Remote Similarity NPC1340
0.5952 Remote Similarity NPC187471
0.5941 Remote Similarity NPC477225
0.5938 Remote Similarity NPC473637
0.5938 Remote Similarity NPC307167
0.5938 Remote Similarity NPC229801
0.5938 Remote Similarity NPC476668
0.5938 Remote Similarity NPC210759
0.5934 Remote Similarity NPC478054
0.5934 Remote Similarity NPC2572
0.5934 Remote Similarity NPC29342
0.5934 Remote Similarity NPC69953
0.593 Remote Similarity NPC243027
0.593 Remote Similarity NPC36479
0.593 Remote Similarity NPC158208
0.593 Remote Similarity NPC317242
0.593 Remote Similarity NPC196136
0.5914 Remote Similarity NPC470657
0.5914 Remote Similarity NPC474448
0.5914 Remote Similarity NPC80700
0.5914 Remote Similarity NPC477283
0.5909 Remote Similarity NPC43463
0.5909 Remote Similarity NPC252483
0.5909 Remote Similarity NPC191345
0.5904 Remote Similarity NPC66407
0.5904 Remote Similarity NPC16964
0.5904 Remote Similarity NPC475062
0.5895 Remote Similarity NPC228059
0.5882 Remote Similarity NPC476709
0.5882 Remote Similarity NPC153719
0.5882 Remote Similarity NPC470610
0.5876 Remote Similarity NPC311246
0.5876 Remote Similarity NPC167644
0.5876 Remote Similarity NPC476669
0.587 Remote Similarity NPC291310
0.5862 Remote Similarity NPC163597
0.5862 Remote Similarity NPC329626
0.5859 Remote Similarity NPC473287
0.5854 Remote Similarity NPC477760
0.5854 Remote Similarity NPC477754
0.5854 Remote Similarity NPC477759
0.5854 Remote Similarity NPC477758
0.5854 Remote Similarity NPC477761
0.5851 Remote Similarity NPC251808
0.5851 Remote Similarity NPC474174
0.5851 Remote Similarity NPC31349
0.5851 Remote Similarity NPC140446
0.5851 Remote Similarity NPC43912
0.5843 Remote Similarity NPC269333
0.5843 Remote Similarity NPC476701
0.5833 Remote Similarity NPC159390
0.5833 Remote Similarity NPC133995
0.5833 Remote Similarity NPC473542
0.5833 Remote Similarity NPC247891
0.5833 Remote Similarity NPC282454
0.5824 Remote Similarity NPC296734
0.5824 Remote Similarity NPC154043
0.5824 Remote Similarity NPC60018
0.5824 Remote Similarity NPC202688
0.5824 Remote Similarity NPC212340
0.5816 Remote Similarity NPC252253
0.5816 Remote Similarity NPC113500
0.5816 Remote Similarity NPC305418
0.5816 Remote Similarity NPC45959
0.5816 Remote Similarity NPC30687
0.5816 Remote Similarity NPC3538
0.5816 Remote Similarity NPC475325
0.5816 Remote Similarity NPC175
0.5816 Remote Similarity NPC477224
0.5814 Remote Similarity NPC308489
0.5814 Remote Similarity NPC475458
0.5814 Remote Similarity NPC477867
0.5814 Remote Similarity NPC228994
0.5814 Remote Similarity NPC192501
0.5814 Remote Similarity NPC48795
0.5814 Remote Similarity NPC10476
0.5806 Remote Similarity NPC470175
0.58 Remote Similarity NPC316604
0.5795 Remote Similarity NPC302578
0.5795 Remote Similarity NPC185915
0.5795 Remote Similarity NPC192046
0.5795 Remote Similarity NPC128951
0.5795 Remote Similarity NPC105208
0.5795 Remote Similarity NPC477227
0.5795 Remote Similarity NPC70996
0.5795 Remote Similarity NPC476703
0.5795 Remote Similarity NPC244002
0.5795 Remote Similarity NPC476719
0.5789 Remote Similarity NPC201607
0.5789 Remote Similarity NPC470009
0.5789 Remote Similarity NPC473436
0.5789 Remote Similarity NPC56777
0.5778 Remote Similarity NPC7479
0.5778 Remote Similarity NPC472951
0.5778 Remote Similarity NPC248944
0.5778 Remote Similarity NPC257296
0.5778 Remote Similarity NPC186588

  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 NPC470630 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
0.6494 Remote Similarity NPD371 Approved
0.5833 Remote Similarity NPD6701 Clinical (unspecified phase)
0.5833 Remote Similarity NPD6700 Approved
0.5778 Remote Similarity NPD6928 Phase 2
0.5773 Remote Similarity NPD6702 Approved
0.5773 Remote Similarity NPD6703 Approved
0.5735 Remote Similarity NPD1462 Approved
0.5714 Remote Similarity NPD4267 Clinical (unspecified phase)
0.5714 Remote Similarity NPD8171 Discontinued
0.5632 Remote Similarity NPD1811 Approved
0.5632 Remote Similarity NPD1810 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