Structure

Physi-Chem Properties

Molecular Weight:  136.06
Volume:  131.126
LogP:  -0.384
LogD:  0.232
LogS:  0.651
# Rotatable Bonds:  5
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.526
Synthetic Accessibility Score:  2.55
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.835
MDCK Permeability:  1.207713739859173e-05
Pgp-inhibitor:  0.025
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.168
20% Bioavailability (F20%):  0.052
30% Bioavailability (F30%):  0.932

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.57
Plasma Protein Binding (PPB):  10.568185806274414%
Volume Distribution (VD):  0.879
Pgp-substrate:  88.07666778564453%

ADMET: Metabolism

CYP1A2-inhibitor:  0.033
CYP1A2-substrate:  0.165
CYP2C19-inhibitor:  0.015
CYP2C19-substrate:  0.337
CYP2C9-inhibitor:  0.003
CYP2C9-substrate:  0.163
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.118
CYP3A4-inhibitor:  0.004
CYP3A4-substrate:  0.135

ADMET: Excretion

Clearance (CL):  6.881
Half-life (T1/2):  0.942

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.08
Drug-inuced Liver Injury (DILI):  0.064
AMES Toxicity:  0.022
Rat Oral Acute Toxicity:  0.009
Maximum Recommended Daily Dose:  0.007
Skin Sensitization:  0.408
Carcinogencity:  0.902
Eye Corrosion:  0.534
Eye Irritation:  0.994
Respiratory Toxicity:  0.021

Download Data

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

  Natural Product: NPC327718

Natural Product ID:  NPC327718
Common Name*:   3-(2-Hydroxyethylsulfanyl)Propan-1-Ol
IUPAC Name:   3-(2-hydroxyethylsulfanyl)propan-1-ol
Synonyms:  
Standard InCHIKey:  YJGRQEWXDDCCCV-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H12O2S/c6-2-1-4-8-5-3-7/h6-7H,1-5H2
SMILES:  OCCSCCCO
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1741874
PubChem CID:   220278
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000004] Organosulfur compounds
      • [CHEMONTID:0001202] Thioethers
        • [CHEMONTID:0003862] Dialkylthioethers

*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
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. Nigeria(latitude 80°N and longitude 4°E) 2005; 2006 DOI[10.1002/ejlt.201000080]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11306-010-0259-y]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11306-014-0638-x]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11746-997-0093-1]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.phytol.2008.07.007]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Seeds Plovdiv, Plovdiv region in South Bulgaria DOI[10.1051/CTV/20163101031]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[11170689]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. fruit n.a. PMID[11312782]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. leaf n.a. PMID[11312782]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[11408943]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. fruit n.a. PMID[12105962]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. Esuela Tecnica Superior de Ingenieros Agrónomos de Albacete 2007 PMID[19256538]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[20826702]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[23759170]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Stalks n.a. n.a. PMID[24521157]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Seeds Benedictine Pannonhalma Archabbey, Hungary PMID[29803478]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[31433178]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Leaf Essent. Oil n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Fruits n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17024 Vitis vinifera Species Vitaceae 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
NPT367 Cell Line MDA-N Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT368 Cell Line SN12C Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT370 Cell Line NCI-H23 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT369 Cell Line ACHN Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT371 Cell Line UO-31 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT372 Cell Line HOP-92 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT116 Cell Line HL-60 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT374 Cell Line SF-539 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT90 Cell Line DU-145 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT373 Cell Line SK-MEL-5 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT375 Cell Line Malme-3M Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT376 Cell Line A498 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT111 Cell Line K562 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT377 Cell Line OVCAR-3 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT112 Cell Line MOLT-4 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT379 Cell Line HOP-62 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT378 Cell Line NCI/ADR-RES Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT380 Cell Line U-251 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT381 Cell Line OVCAR-8 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT382 Cell Line OVCAR-5 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT383 Cell Line SNB-19 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT82 Cell Line MDA-MB-231 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT385 Cell Line SR Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT384 Cell Line TK-10 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT323 Cell Line SW-620 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT455 Cell Line NCI-H522 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT386 Cell Line KM12 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT387 Cell Line M14 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT388 Cell Line NCI-H322M Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT389 Cell Line RPMI-8226 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT390 Cell Line LOX IMVI Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT456 Cell Line OVCAR-4 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT457 Cell Line BT-549 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT147 Cell Line SK-MEL-2 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT81 Cell Line A549 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT392 Cell Line SNB-75 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT391 Cell Line HCC 2998 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT393 Cell Line HCT-116 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT148 Cell Line HCT-15 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT395 Cell Line SF-268 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT394 Cell Line EKVX Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT83 Cell Line MCF7 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT306 Cell Line PC-3 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT146 Cell Line SK-OV-3 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT396 Cell Line T47D Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT398 Cell Line UACC-62 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT397 Cell Line NCI-H460 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT308 Cell Line CAKI-1 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT400 Cell Line MDA-MB-435 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT458 Cell Line IGROV-1 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT399 Cell Line SF-295 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT402 Cell Line Hs-578T Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT401 Cell Line 786-0 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT403 Cell Line UACC-257 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT404 Cell Line CCRF-CEM Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT405 Cell Line NCI-H226 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT139 Cell Line HT-29 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT170 Cell Line SK-MEL-28 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]
NPT407 Cell Line COLO 205 Homo sapiens GI50 n.a. 100000.0 nM PMID[481479]

☑ 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 NPC327718 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
0.8929 High Similarity NPC261397
0.75 Intermediate Similarity NPC317406
0.697 Remote Similarity NPC317060
0.6765 Remote Similarity NPC14778
0.6429 Remote Similarity NPC85721
0.6364 Remote Similarity NPC162547
0.6207 Remote Similarity NPC219266
0.6071 Remote Similarity NPC236761
0.6061 Remote Similarity NPC319333
0.5862 Remote Similarity NPC294703
0.5806 Remote Similarity NPC94144
0.5806 Remote Similarity NPC87529
0.5806 Remote Similarity NPC199270
0.5758 Remote Similarity NPC327450
0.575 Remote Similarity NPC329545
0.5714 Remote Similarity NPC16947
0.5714 Remote Similarity NPC311000
0.5667 Remote Similarity NPC299484
0.5667 Remote Similarity NPC110344
0.5667 Remote Similarity NPC88839
0.5641 Remote Similarity NPC325038
0.5625 Remote Similarity NPC140389
0.5625 Remote Similarity NPC213764
0.5625 Remote Similarity NPC88887

  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 NPC327718 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
0.7241 Intermediate Similarity NPD8231 Approved
0.6 Remote Similarity NPD9669 Clinical (unspecified phase)
0.587 Remote Similarity NPD9025 Approved
0.5714 Remote Similarity NPD8223 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