Structure

Physi-Chem Properties

Molecular Weight:  474.37
Volume:  546.778
LogP:  5.202
LogD:  4.144
LogS:  -3.527
# Rotatable Bonds:  19
TPSA:  80.92
# H-Bond Aceptor:  4
# H-Bond Donor:  4
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.127
Synthetic Accessibility Score:  3.337
Fsp3:  0.6
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.724
MDCK Permeability:  2.2089958292781375e-05
Pgp-inhibitor:  0.247
Pgp-substrate:  0.007
Human Intestinal Absorption (HIA):  0.05
20% Bioavailability (F20%):  0.915
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.337
Plasma Protein Binding (PPB):  92.20160675048828%
Volume Distribution (VD):  0.94
Pgp-substrate:  0.8101235032081604%

ADMET: Metabolism

CYP1A2-inhibitor:  0.081
CYP1A2-substrate:  0.053
CYP2C19-inhibitor:  0.027
CYP2C19-substrate:  0.037
CYP2C9-inhibitor:  0.021
CYP2C9-substrate:  0.048
CYP2D6-inhibitor:  0.616
CYP2D6-substrate:  0.051
CYP3A4-inhibitor:  0.374
CYP3A4-substrate:  0.095

ADMET: Excretion

Clearance (CL):  4.79
Half-life (T1/2):  0.886

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.042
Drug-inuced Liver Injury (DILI):  0.021
AMES Toxicity:  0.0
Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.923
Skin Sensitization:  0.987
Carcinogencity:  0.019
Eye Corrosion:  0.005
Eye Irritation:  0.867
Respiratory Toxicity:  0.009

Download Data

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

  Natural Product: NPC160628

Natural Product ID:  NPC160628
Common Name*:   Tetrahydroxysqualene
IUPAC Name:   (6E,10E,14E,18E)-2,23-bis(hydroxymethyl)-6,10,15,19-tetramethyltetracosa-2,6,10,14,18,22-hexaene-1,24-diol
Synonyms:   tetrahydroxysqualene
Standard InCHIKey:  YMMHDITUHQNNKU-DKTKHUEWSA-N
Standard InCHI:  InChI=1S/C30H50O4/c1-25(13-7-15-27(3)17-9-19-29(21-31)22-32)11-5-6-12-26(2)14-8-16-28(4)18-10-20-30(23-33)24-34/h11-12,15-16,19-20,31-34H,5-10,13-14,17-18,21-24H2,1-4H3/b25-11+,26-12+,27-15+,28-16+
SMILES:  OCC(=CCC/C(=C/CC/C(=C/CC/C=C(/CC/C=C(/CCC=C(CO)CO)C)C)/C)/C)CO
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL498335
PubChem CID:   25058109
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

*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
NPO30411 Rhus taitensis Species Anacardiaceae Eukaryota n.a. twig n.a. PMID[18710283]
NPO30411 Rhus taitensis Species Anacardiaceae Eukaryota n.a. leaf n.a. PMID[18710283]

☑ 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
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC = 10.0 ug.mL-1 PMID[524168]
NPT27 Others Unspecified EC50 = 27.5 ug.mL-1 PMID[524168]

☑ 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 NPC160628 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
0.9524 High Similarity NPC116934
0.9091 High Similarity NPC140501
0.9048 High Similarity NPC269823
0.8837 High Similarity NPC213538
0.8837 High Similarity NPC256766
0.8571 High Similarity NPC103213
0.8571 High Similarity NPC29091
0.8571 High Similarity NPC255042
0.8571 High Similarity NPC182840
0.8444 Intermediate Similarity NPC138935
0.8333 Intermediate Similarity NPC474460
0.82 Intermediate Similarity NPC474496
0.8163 Intermediate Similarity NPC473672
0.8163 Intermediate Similarity NPC474495
0.8125 Intermediate Similarity NPC267110
0.7727 Intermediate Similarity NPC15934
0.76 Intermediate Similarity NPC26960
0.76 Intermediate Similarity NPC182102
0.7551 Intermediate Similarity NPC318549
0.7455 Intermediate Similarity NPC181872
0.7455 Intermediate Similarity NPC223679
0.74 Intermediate Similarity NPC153538
0.7347 Intermediate Similarity NPC308331
0.7321 Intermediate Similarity NPC475931
0.7308 Intermediate Similarity NPC35756
0.7273 Intermediate Similarity NPC249850
0.7273 Intermediate Similarity NPC129150
0.7273 Intermediate Similarity NPC135863
0.7273 Intermediate Similarity NPC268185
0.7273 Intermediate Similarity NPC293437
0.7255 Intermediate Similarity NPC72699
0.7255 Intermediate Similarity NPC291437
0.7255 Intermediate Similarity NPC328784
0.7234 Intermediate Similarity NPC304151
0.7234 Intermediate Similarity NPC206906
0.7222 Intermediate Similarity NPC329686
0.7209 Intermediate Similarity NPC58957
0.717 Intermediate Similarity NPC217188
0.7143 Intermediate Similarity NPC254095
0.7143 Intermediate Similarity NPC226848
0.7143 Intermediate Similarity NPC221379
0.7143 Intermediate Similarity NPC269074
0.7115 Intermediate Similarity NPC244038
0.7115 Intermediate Similarity NPC151782
0.7115 Intermediate Similarity NPC93639
0.7115 Intermediate Similarity NPC71053
0.7115 Intermediate Similarity NPC59408
0.7115 Intermediate Similarity NPC55383
0.7111 Intermediate Similarity NPC34873
0.7111 Intermediate Similarity NPC40434
0.7069 Intermediate Similarity NPC55376
0.7059 Intermediate Similarity NPC31194
0.7059 Intermediate Similarity NPC85079
0.7059 Intermediate Similarity NPC248884
0.7037 Intermediate Similarity NPC189677
0.7018 Intermediate Similarity NPC122239
0.7 Intermediate Similarity NPC35141
0.7 Intermediate Similarity NPC180575
0.7 Intermediate Similarity NPC124183
0.7 Intermediate Similarity NPC282760
0.6977 Remote Similarity NPC250734
0.6964 Remote Similarity NPC52012
0.6964 Remote Similarity NPC294938
0.6939 Remote Similarity NPC6963
0.6939 Remote Similarity NPC304079
0.6923 Remote Similarity NPC249670
0.6923 Remote Similarity NPC199286
0.6923 Remote Similarity NPC474642
0.6923 Remote Similarity NPC471281
0.6923 Remote Similarity NPC288381
0.6923 Remote Similarity NPC225974
0.6923 Remote Similarity NPC20934
0.6923 Remote Similarity NPC477727
0.6923 Remote Similarity NPC473913
0.6909 Remote Similarity NPC281590
0.6897 Remote Similarity NPC130807
0.6875 Remote Similarity NPC108494
0.6875 Remote Similarity NPC180871
0.6875 Remote Similarity NPC209279
0.6875 Remote Similarity NPC194586
0.6875 Remote Similarity NPC51758
0.6875 Remote Similarity NPC67761
0.6875 Remote Similarity NPC88079
0.6875 Remote Similarity NPC68889
0.6842 Remote Similarity NPC21946
0.6809 Remote Similarity NPC56917
0.68 Remote Similarity NPC210560
0.68 Remote Similarity NPC76976
0.68 Remote Similarity NPC24824
0.68 Remote Similarity NPC165651
0.6792 Remote Similarity NPC197272
0.6792 Remote Similarity NPC170776
0.6792 Remote Similarity NPC475477
0.6792 Remote Similarity NPC129263
0.6792 Remote Similarity NPC165447
0.6792 Remote Similarity NPC76198
0.6792 Remote Similarity NPC329608
0.6792 Remote Similarity NPC471959
0.6792 Remote Similarity NPC89824
0.6792 Remote Similarity NPC294278
0.6792 Remote Similarity NPC224148
0.6792 Remote Similarity NPC256656
0.6792 Remote Similarity NPC9273
0.6792 Remote Similarity NPC477723
0.678 Remote Similarity NPC29468
0.6731 Remote Similarity NPC471280
0.6731 Remote Similarity NPC471276
0.6731 Remote Similarity NPC471275
0.6731 Remote Similarity NPC125122
0.6727 Remote Similarity NPC110732
0.6727 Remote Similarity NPC256209
0.6727 Remote Similarity NPC49059
0.6727 Remote Similarity NPC473532
0.6724 Remote Similarity NPC82465
0.6724 Remote Similarity NPC322186
0.6721 Remote Similarity NPC477525
0.6667 Remote Similarity NPC283502
0.6667 Remote Similarity NPC197467
0.6667 Remote Similarity NPC71755
0.6667 Remote Similarity NPC142092
0.6667 Remote Similarity NPC19834
0.6667 Remote Similarity NPC242117
0.6667 Remote Similarity NPC11130
0.6667 Remote Similarity NPC470970
0.6667 Remote Similarity NPC55063
0.661 Remote Similarity NPC258788
0.661 Remote Similarity NPC471081
0.6607 Remote Similarity NPC473910
0.6607 Remote Similarity NPC474644
0.6607 Remote Similarity NPC227135
0.6607 Remote Similarity NPC473721
0.6607 Remote Similarity NPC477726
0.6607 Remote Similarity NPC475353
0.6607 Remote Similarity NPC130209
0.6607 Remote Similarity NPC148216
0.6607 Remote Similarity NPC232247
0.6607 Remote Similarity NPC148163
0.6607 Remote Similarity NPC473725
0.6607 Remote Similarity NPC251666
0.6607 Remote Similarity NPC477725
0.6607 Remote Similarity NPC473735
0.6607 Remote Similarity NPC298299
0.6607 Remote Similarity NPC473896
0.66 Remote Similarity NPC108195
0.66 Remote Similarity NPC101616
0.66 Remote Similarity NPC12907
0.6552 Remote Similarity NPC155025
0.6545 Remote Similarity NPC61177
0.6545 Remote Similarity NPC34577
0.6508 Remote Similarity NPC73603
0.6491 Remote Similarity NPC470966
0.6491 Remote Similarity NPC48891
0.6491 Remote Similarity NPC471960
0.6491 Remote Similarity NPC473847
0.6491 Remote Similarity NPC55412
0.6491 Remote Similarity NPC470968
0.6491 Remote Similarity NPC470967
0.6491 Remote Similarity NPC475384
0.6491 Remote Similarity NPC249645
0.6491 Remote Similarity NPC474643
0.6491 Remote Similarity NPC470969
0.6491 Remote Similarity NPC161838
0.6491 Remote Similarity NPC473865
0.6491 Remote Similarity NPC477661
0.6481 Remote Similarity NPC43053
0.6481 Remote Similarity NPC200772
0.6471 Remote Similarity NPC47946
0.6471 Remote Similarity NPC26600
0.6471 Remote Similarity NPC276825
0.6458 Remote Similarity NPC329762
0.6458 Remote Similarity NPC103236
0.6458 Remote Similarity NPC27444
0.6452 Remote Similarity NPC308844
0.6441 Remote Similarity NPC322002
0.6441 Remote Similarity NPC318306
0.6429 Remote Similarity NPC48058
0.6429 Remote Similarity NPC123965
0.6429 Remote Similarity NPC115959
0.6415 Remote Similarity NPC302310
0.6415 Remote Similarity NPC62755
0.64 Remote Similarity NPC252978
0.6393 Remote Similarity NPC124112
0.6393 Remote Similarity NPC68110
0.6393 Remote Similarity NPC55068
0.6393 Remote Similarity NPC471023
0.6379 Remote Similarity NPC48968
0.6379 Remote Similarity NPC594
0.6379 Remote Similarity NPC472445
0.6364 Remote Similarity NPC208638
0.6364 Remote Similarity NPC316185
0.6364 Remote Similarity NPC197356
0.6364 Remote Similarity NPC63121
0.6349 Remote Similarity NPC129995
0.6349 Remote Similarity NPC315141
0.6349 Remote Similarity NPC146811
0.6346 Remote Similarity NPC157096
0.6346 Remote Similarity NPC128280
0.6333 Remote Similarity NPC99487
0.6333 Remote Similarity NPC240506
0.6333 Remote Similarity NPC66020

  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 NPC160628 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
0.9091 High Similarity NPD4265 Approved
0.6923 Remote Similarity NPD2268 Discontinued
0.6731 Remote Similarity NPD4220 Pre-registration
0.6607 Remote Similarity NPD342 Phase 1
0.6552 Remote Similarity NPD585 Clinical (unspecified phase)
0.6491 Remote Similarity NPD4219 Approved
0.6481 Remote Similarity NPD6927 Phase 3
0.6393 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6333 Remote Similarity NPD4246 Clinical (unspecified phase)
0.625 Remote Similarity NPD5783 Phase 3
0.623 Remote Similarity NPD368 Approved
0.6154 Remote Similarity NPD39 Approved
0.6078 Remote Similarity NPD5326 Phase 3
0.6 Remote Similarity NPD4247 Clinical (unspecified phase)
0.597 Remote Similarity NPD3212 Clinical (unspecified phase)
0.5849 Remote Similarity NPD4222 Approved
0.58 Remote Similarity NPD1153 Clinical (unspecified phase)
0.5797 Remote Similarity NPD4732 Discontinued
0.5769 Remote Similarity NPD9411 Phase 1
0.566 Remote Similarity NPD6096 Approved
0.566 Remote Similarity NPD6097 Approved
0.5636 Remote Similarity NPD5343 Approved
0.5634 Remote Similarity NPD8264 Approved
0.5616 Remote Similarity NPD4268 Approved
0.5616 Remote Similarity NPD4271 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