Structure

Physi-Chem Properties

Molecular Weight:  238.19
Volume:  259.907
LogP:  3.564
LogD:  3.718
LogS:  -3.753
# Rotatable Bonds:  0
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.681
Synthetic Accessibility Score:  4.598
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.724
MDCK Permeability:  3.962432674597949e-05
Pgp-inhibitor:  0.011
Pgp-substrate:  0.006
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.011

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.309
Plasma Protein Binding (PPB):  73.72470092773438%
Volume Distribution (VD):  0.899
Pgp-substrate:  29.186552047729492%

ADMET: Metabolism

CYP1A2-inhibitor:  0.051
CYP1A2-substrate:  0.229
CYP2C19-inhibitor:  0.039
CYP2C19-substrate:  0.885
CYP2C9-inhibitor:  0.11
CYP2C9-substrate:  0.477
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.327
CYP3A4-inhibitor:  0.13
CYP3A4-substrate:  0.296

ADMET: Excretion

Clearance (CL):  7.382
Half-life (T1/2):  0.437

ADMET: Toxicity

hERG Blockers:  0.048
Human Hepatotoxicity (H-HT):  0.22
Drug-inuced Liver Injury (DILI):  0.029
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.927
Maximum Recommended Daily Dose:  0.675
Skin Sensitization:  0.352
Carcinogencity:  0.035
Eye Corrosion:  0.866
Eye Irritation:  0.864
Respiratory Toxicity:  0.963

Download Data

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

  Natural Product: NPC161473

Natural Product ID:  NPC161473
Common Name*:   Tricyclohumuladiol
IUPAC Name:   n.a.
Synonyms:   Tricyclohumuladiol
Standard InCHIKey:  USFOCJBPTUMHRF-DNNYSMPMSA-N
Standard InCHI:  InChI=1S/C15H26O2/c1-13(2)7-10-12(13)9-8-14(9,3)11(16)5-6-15(10,4)17/h9-12,16-17H,5-8H2,1-4H3/t9-,10+,11-,12-,14-,15+/m1/s1
SMILES:  CC1(C)C[C@H]2[C@H]1[C@H]1C[C@@]1(C)[C@@H](CC[C@]2(C)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL465350
PubChem CID:   15647027
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
NPO12458 Zingiber aromaticum Species Zingiberaceae Eukaryota n.a. rhizome n.a. DOI[10.1080/10575639708043725]
NPO7630 Cyperus longus Species Cyperaceae Eukaryota n.a. Egyptian herbal medicine n.a. PMID[15104485]
NPO12458 Zingiber aromaticum Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[15270556]
NPO12458 Zingiber aromaticum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12458 Zingiber aromaticum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7630 Cyperus longus Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12458 Zingiber aromaticum Species Zingiberaceae 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
NPT993 Cell Line Hepatocyte Mus musculus Inhibition = 37.7 % PMID[523852]
NPT993 Cell Line Hepatocyte Mus musculus Inhibition = 22.1 % PMID[523852]
NPT993 Cell Line Hepatocyte Mus musculus Inhibition = 16.1 % PMID[523852]
NPT993 Cell Line Hepatocyte Mus musculus Inhibition = 10.9 % PMID[523852]

☑ 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 NPC161473 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
0.7759 Intermediate Similarity NPC87296
0.7759 Intermediate Similarity NPC475515
0.7759 Intermediate Similarity NPC215671
0.7667 Intermediate Similarity NPC475807
0.7586 Intermediate Similarity NPC291147
0.7544 Intermediate Similarity NPC471269
0.75 Intermediate Similarity NPC475412
0.7368 Intermediate Similarity NPC53209
0.7143 Intermediate Similarity NPC307022
0.7115 Intermediate Similarity NPC144891
0.7097 Intermediate Similarity NPC185547
0.7097 Intermediate Similarity NPC95804
0.7091 Intermediate Similarity NPC95969
0.7091 Intermediate Similarity NPC127997
0.7091 Intermediate Similarity NPC294858
0.7037 Intermediate Similarity NPC176309
0.7037 Intermediate Similarity NPC147343
0.7037 Intermediate Similarity NPC84030
0.7037 Intermediate Similarity NPC223468
0.7037 Intermediate Similarity NPC198540
0.7037 Intermediate Similarity NPC287550
0.7 Intermediate Similarity NPC236588
0.6949 Remote Similarity NPC45387
0.6939 Remote Similarity NPC177022
0.6875 Remote Similarity NPC199937
0.6818 Remote Similarity NPC33583
0.6818 Remote Similarity NPC161612
0.678 Remote Similarity NPC286752
0.6774 Remote Similarity NPC475968
0.6769 Remote Similarity NPC61503
0.6735 Remote Similarity NPC61665
0.6735 Remote Similarity NPC328441
0.6721 Remote Similarity NPC135438
0.6721 Remote Similarity NPC119425
0.6667 Remote Similarity NPC283655
0.6667 Remote Similarity NPC178223
0.6667 Remote Similarity NPC300189
0.6667 Remote Similarity NPC89069
0.6667 Remote Similarity NPC240994
0.6667 Remote Similarity NPC277917
0.6667 Remote Similarity NPC166894
0.6667 Remote Similarity NPC221022
0.6562 Remote Similarity NPC172622
0.6552 Remote Similarity NPC474331
0.6545 Remote Similarity NPC77550
0.6545 Remote Similarity NPC108441
0.6545 Remote Similarity NPC473914
0.6515 Remote Similarity NPC472946
0.6515 Remote Similarity NPC165069
0.6508 Remote Similarity NPC185116
0.6462 Remote Similarity NPC50435
0.6452 Remote Similarity NPC150713
0.6452 Remote Similarity NPC27853
0.6452 Remote Similarity NPC65786
0.6452 Remote Similarity NPC13789
0.6452 Remote Similarity NPC29976
0.6452 Remote Similarity NPC7491
0.6452 Remote Similarity NPC101285
0.6429 Remote Similarity NPC14552
0.6377 Remote Similarity NPC299948
0.6377 Remote Similarity NPC241085
0.6377 Remote Similarity NPC470830
0.6364 Remote Similarity NPC69149
0.6364 Remote Similarity NPC101128
0.6364 Remote Similarity NPC219940
0.6364 Remote Similarity NPC476702
0.6364 Remote Similarity NPC215358
0.6349 Remote Similarity NPC47663
0.6338 Remote Similarity NPC329763
0.6333 Remote Similarity NPC102336
0.6333 Remote Similarity NPC36002
0.6327 Remote Similarity NPC283682
0.6324 Remote Similarity NPC139207
0.6324 Remote Similarity NPC185874
0.6324 Remote Similarity NPC475884
0.6324 Remote Similarity NPC473230
0.6308 Remote Similarity NPC253204
0.6269 Remote Similarity NPC2728
0.6269 Remote Similarity NPC80463
0.6269 Remote Similarity NPC11555
0.6269 Remote Similarity NPC172613
0.6269 Remote Similarity NPC60837
0.6269 Remote Similarity NPC474380
0.6269 Remote Similarity NPC260116
0.6269 Remote Similarity NPC208198
0.6269 Remote Similarity NPC41577
0.6269 Remote Similarity NPC476330
0.6269 Remote Similarity NPC282619
0.6269 Remote Similarity NPC473276
0.6232 Remote Similarity NPC472741
0.6226 Remote Similarity NPC160261
0.6226 Remote Similarity NPC469759
0.6212 Remote Similarity NPC236099
0.6212 Remote Similarity NPC249078
0.6212 Remote Similarity NPC114891
0.6212 Remote Similarity NPC474155
0.6212 Remote Similarity NPC209686
0.6212 Remote Similarity NPC473759
0.6197 Remote Similarity NPC473279
0.6197 Remote Similarity NPC195530
0.6176 Remote Similarity NPC473899
0.6176 Remote Similarity NPC473929
0.6176 Remote Similarity NPC475897
0.6176 Remote Similarity NPC44122
0.6143 Remote Similarity NPC470833
0.6143 Remote Similarity NPC66407
0.6122 Remote Similarity NPC319034
0.6122 Remote Similarity NPC72324
0.6122 Remote Similarity NPC193062
0.6122 Remote Similarity NPC66124
0.6122 Remote Similarity NPC1748
0.6119 Remote Similarity NPC94897
0.6119 Remote Similarity NPC281540
0.6119 Remote Similarity NPC159654
0.6119 Remote Similarity NPC167995
0.6119 Remote Similarity NPC300593
0.6119 Remote Similarity NPC144650
0.6119 Remote Similarity NPC118937
0.6111 Remote Similarity NPC472341
0.6111 Remote Similarity NPC310608
0.6111 Remote Similarity NPC473238
0.6094 Remote Similarity NPC476735
0.6087 Remote Similarity NPC48079
0.6087 Remote Similarity NPC476928
0.6087 Remote Similarity NPC253303
0.6087 Remote Similarity NPC269077
0.6078 Remote Similarity NPC474392
0.6078 Remote Similarity NPC474914
0.6061 Remote Similarity NPC148174
0.6061 Remote Similarity NPC475251
0.6061 Remote Similarity NPC71460
0.6061 Remote Similarity NPC218585
0.6056 Remote Similarity NPC282454
0.6056 Remote Similarity NPC133873
0.6034 Remote Similarity NPC314087
0.6032 Remote Similarity NPC170780
0.6032 Remote Similarity NPC24443
0.6029 Remote Similarity NPC243469
0.6029 Remote Similarity NPC471200
0.6029 Remote Similarity NPC190827
0.6029 Remote Similarity NPC258595
0.6029 Remote Similarity NPC475943
0.6029 Remote Similarity NPC300442
0.6 Remote Similarity NPC276616
0.6 Remote Similarity NPC244790
0.6 Remote Similarity NPC471238
0.6 Remote Similarity NPC475031
0.6 Remote Similarity NPC95958
0.6 Remote Similarity NPC184049
0.6 Remote Similarity NPC474954
0.6 Remote Similarity NPC474756
0.6 Remote Similarity NPC245795
0.6 Remote Similarity NPC99480
0.6 Remote Similarity NPC188793
0.6 Remote Similarity NPC475893
0.5972 Remote Similarity NPC470071
0.5972 Remote Similarity NPC127094
0.5972 Remote Similarity NPC100586
0.5972 Remote Similarity NPC164022
0.5972 Remote Similarity NPC1340
0.5972 Remote Similarity NPC187471
0.5972 Remote Similarity NPC471662
0.5972 Remote Similarity NPC157422
0.5972 Remote Similarity NPC471272
0.5972 Remote Similarity NPC252182
0.5972 Remote Similarity NPC109457
0.597 Remote Similarity NPC133368
0.597 Remote Similarity NPC292419
0.597 Remote Similarity NPC83200
0.597 Remote Similarity NPC211291
0.597 Remote Similarity NPC290791
0.5968 Remote Similarity NPC32222
0.5968 Remote Similarity NPC202146
0.5965 Remote Similarity NPC87439
0.5946 Remote Similarity NPC472952
0.5946 Remote Similarity NPC472950
0.5942 Remote Similarity NPC469328
0.5942 Remote Similarity NPC142712
0.5942 Remote Similarity NPC476406
0.5938 Remote Similarity NPC322148
0.5921 Remote Similarity NPC471769
0.5921 Remote Similarity NPC475980
0.5921 Remote Similarity NPC147993
0.5918 Remote Similarity NPC122962
0.5918 Remote Similarity NPC267243
0.5915 Remote Similarity NPC99264
0.5915 Remote Similarity NPC9942
0.5915 Remote Similarity NPC474248
0.5915 Remote Similarity NPC477820
0.5915 Remote Similarity NPC210323
0.5915 Remote Similarity NPC107919
0.5915 Remote Similarity NPC254037
0.5915 Remote Similarity NPC129829
0.589 Remote Similarity NPC95165
0.589 Remote Similarity NPC253805
0.5882 Remote Similarity NPC68656
0.5882 Remote Similarity NPC225415
0.5882 Remote Similarity NPC128608
0.5882 Remote Similarity NPC97967
0.5882 Remote Similarity NPC309300

  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 NPC161473 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
0.7037 Intermediate Similarity NPD385 Approved
0.7037 Intermediate Similarity NPD384 Approved
0.6545 Remote Similarity NPD386 Approved
0.6545 Remote Similarity NPD388 Approved
0.6296 Remote Similarity NPD1462 Approved
0.6226 Remote Similarity NPD1460 Approved
0.6119 Remote Similarity NPD371 Approved
0.5968 Remote Similarity NPD3729 Clinical (unspecified phase)
0.5915 Remote Similarity NPD4267 Clinical (unspecified phase)
0.5833 Remote Similarity NPD4787 Phase 1
0.5797 Remote Similarity NPD3171 Clinical (unspecified phase)
0.5758 Remote Similarity NPD3198 Approved
0.5694 Remote Similarity NPD3699 Clinical (unspecified phase)
0.5694 Remote Similarity NPD3700 Clinical (unspecified phase)
0.5694 Remote Similarity NPD3698 Phase 2
0.5616 Remote Similarity NPD4245 Approved
0.5616 Remote Similarity NPD4244 Approved
0.5614 Remote Similarity NPD367 Approved
0.56 Remote Similarity NPD6926 Approved
0.56 Remote Similarity NPD6924 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