Structure

Physi-Chem Properties

Molecular Weight:  238.19
Volume:  259.907
LogP:  3.515
LogD:  3.236
LogS:  -3.604
# 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:  5.127
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:  -4.747
MDCK Permeability:  3.408731208764948e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.023
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.013

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.195
Plasma Protein Binding (PPB):  86.91596984863281%
Volume Distribution (VD):  1.219
Pgp-substrate:  20.804779052734375%

ADMET: Metabolism

CYP1A2-inhibitor:  0.034
CYP1A2-substrate:  0.403
CYP2C19-inhibitor:  0.056
CYP2C19-substrate:  0.823
CYP2C9-inhibitor:  0.135
CYP2C9-substrate:  0.734
CYP2D6-inhibitor:  0.014
CYP2D6-substrate:  0.432
CYP3A4-inhibitor:  0.42
CYP3A4-substrate:  0.166

ADMET: Excretion

Clearance (CL):  6.347
Half-life (T1/2):  0.317

ADMET: Toxicity

hERG Blockers:  0.054
Human Hepatotoxicity (H-HT):  0.196
Drug-inuced Liver Injury (DILI):  0.027
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.396
Maximum Recommended Daily Dose:  0.86
Skin Sensitization:  0.813
Carcinogencity:  0.056
Eye Corrosion:  0.741
Eye Irritation:  0.922
Respiratory Toxicity:  0.944

Download Data

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

  Natural Product: NPC87296

Natural Product ID:  NPC87296
Common Name*:   SFJOMLIUSIKKRA-FWZIUSJTSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SFJOMLIUSIKKRA-FWZIUSJTSA-N
Standard InCHI:  InChI=1S/C15H26O2/c1-13(2)8-11-10(13)4-6-14(3)9-15(11,17)7-5-12(14)16/h10-12,16-17H,4-9H2,1-3H3/t10-,11-,12-,14-,15+/m1/s1
SMILES:  CC1(C)C[C@@H]2[C@H]1CC[C@]1(C)C[C@]2(CC[C@H]1O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3138629
PubChem CID:   76325936
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001670] Tertiary alcohols

*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
NPO11820 Amomum villosum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11820 Amomum villosum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11820 Amomum villosum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11820 Amomum villosum 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
NPT73 Individual Protein Solute carrier organic anion transporter family member 1B1 Homo sapiens Inhibition = 81.35 % PMID[449389]
NPT72 Individual Protein Solute carrier organic anion transporter family member 1B3 Homo sapiens Inhibition = 87.7 % PMID[449389]

☑ 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 NPC87296 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
1.0 High Similarity NPC475515
1.0 High Similarity NPC215671
0.9091 High Similarity NPC471269
0.8571 High Similarity NPC53209
0.8333 Intermediate Similarity NPC294858
0.8136 Intermediate Similarity NPC236588
0.7833 Intermediate Similarity NPC135438
0.7812 Intermediate Similarity NPC80463
0.7759 Intermediate Similarity NPC161473
0.7719 Intermediate Similarity NPC307022
0.7636 Intermediate Similarity NPC223468
0.7636 Intermediate Similarity NPC287550
0.7636 Intermediate Similarity NPC176309
0.7636 Intermediate Similarity NPC84030
0.7636 Intermediate Similarity NPC147343
0.7636 Intermediate Similarity NPC198540
0.7619 Intermediate Similarity NPC185547
0.7619 Intermediate Similarity NPC95804
0.7576 Intermediate Similarity NPC139207
0.7576 Intermediate Similarity NPC185874
0.75 Intermediate Similarity NPC300189
0.746 Intermediate Similarity NPC475412
0.7419 Intermediate Similarity NPC47663
0.7407 Intermediate Similarity NPC144891
0.7385 Intermediate Similarity NPC94897
0.7302 Intermediate Similarity NPC185116
0.7273 Intermediate Similarity NPC260116
0.7273 Intermediate Similarity NPC240994
0.7206 Intermediate Similarity NPC472741
0.7167 Intermediate Similarity NPC102336
0.7167 Intermediate Similarity NPC36002
0.7164 Intermediate Similarity NPC44122
0.7164 Intermediate Similarity NPC473929
0.7143 Intermediate Similarity NPC164022
0.7143 Intermediate Similarity NPC471272
0.7121 Intermediate Similarity NPC144650
0.7121 Intermediate Similarity NPC101128
0.7101 Intermediate Similarity NPC66407
0.7101 Intermediate Similarity NPC470833
0.7077 Intermediate Similarity NPC475807
0.7059 Intermediate Similarity NPC476928
0.7059 Intermediate Similarity NPC48079
0.7059 Intermediate Similarity NPC269077
0.7059 Intermediate Similarity NPC253303
0.7042 Intermediate Similarity NPC253805
0.7018 Intermediate Similarity NPC14552
0.7015 Intermediate Similarity NPC2728
0.7015 Intermediate Similarity NPC208198
0.7015 Intermediate Similarity NPC282619
0.7015 Intermediate Similarity NPC11555
0.7015 Intermediate Similarity NPC60837
0.7015 Intermediate Similarity NPC172613
0.7 Intermediate Similarity NPC282454
0.6984 Remote Similarity NPC291147
0.697 Remote Similarity NPC114891
0.697 Remote Similarity NPC236099
0.697 Remote Similarity NPC292419
0.697 Remote Similarity NPC209686
0.697 Remote Similarity NPC290791
0.697 Remote Similarity NPC249078
0.6957 Remote Similarity NPC474756
0.6957 Remote Similarity NPC244790
0.6957 Remote Similarity NPC475893
0.6944 Remote Similarity NPC470151
0.6912 Remote Similarity NPC142712
0.6912 Remote Similarity NPC475897
0.6901 Remote Similarity NPC1340
0.6901 Remote Similarity NPC127094
0.6901 Remote Similarity NPC470071
0.6901 Remote Similarity NPC157422
0.6901 Remote Similarity NPC187471
0.6901 Remote Similarity NPC252182
0.6901 Remote Similarity NPC109457
0.6901 Remote Similarity NPC100586
0.6897 Remote Similarity NPC314087
0.6866 Remote Similarity NPC219940
0.6866 Remote Similarity NPC167995
0.6866 Remote Similarity NPC281540
0.6866 Remote Similarity NPC118937
0.6866 Remote Similarity NPC159654
0.6857 Remote Similarity NPC299948
0.6857 Remote Similarity NPC477820
0.6857 Remote Similarity NPC254037
0.6857 Remote Similarity NPC241085
0.6857 Remote Similarity NPC210323
0.6857 Remote Similarity NPC470830
0.6857 Remote Similarity NPC107919
0.6857 Remote Similarity NPC129829
0.6849 Remote Similarity NPC131584
0.6849 Remote Similarity NPC139765
0.6842 Remote Similarity NPC108441
0.6842 Remote Similarity NPC77550
0.6818 Remote Similarity NPC218585
0.6818 Remote Similarity NPC148174
0.6818 Remote Similarity NPC71460
0.6812 Remote Similarity NPC475884
0.6812 Remote Similarity NPC204233
0.6812 Remote Similarity NPC472984
0.6812 Remote Similarity NPC473230
0.6806 Remote Similarity NPC95165
0.6806 Remote Similarity NPC476422
0.6774 Remote Similarity NPC32222
0.6774 Remote Similarity NPC202146
0.6769 Remote Similarity NPC475968
0.6765 Remote Similarity NPC473276
0.6765 Remote Similarity NPC258595
0.6765 Remote Similarity NPC474380
0.6765 Remote Similarity NPC472946
0.6765 Remote Similarity NPC41577
0.6761 Remote Similarity NPC63588
0.6761 Remote Similarity NPC92801
0.6761 Remote Similarity NPC231945
0.6761 Remote Similarity NPC232925
0.6761 Remote Similarity NPC192192
0.6761 Remote Similarity NPC251201
0.6757 Remote Similarity NPC1973
0.6757 Remote Similarity NPC167873
0.6753 Remote Similarity NPC473257
0.6721 Remote Similarity NPC300235
0.6721 Remote Similarity NPC476136
0.6721 Remote Similarity NPC476149
0.6721 Remote Similarity NPC244869
0.6719 Remote Similarity NPC150713
0.6719 Remote Similarity NPC119425
0.6719 Remote Similarity NPC29976
0.6714 Remote Similarity NPC276616
0.6714 Remote Similarity NPC245795
0.6714 Remote Similarity NPC471238
0.6714 Remote Similarity NPC469987
0.6714 Remote Similarity NPC2648
0.6712 Remote Similarity NPC10476
0.6712 Remote Similarity NPC237510
0.6712 Remote Similarity NPC304499
0.6712 Remote Similarity NPC228994
0.6712 Remote Similarity NPC192501
0.6712 Remote Similarity NPC475793
0.6712 Remote Similarity NPC74639
0.6712 Remote Similarity NPC475458
0.6667 Remote Similarity NPC167706
0.6667 Remote Similarity NPC157777
0.6667 Remote Similarity NPC307865
0.6667 Remote Similarity NPC283655
0.6667 Remote Similarity NPC473279
0.6667 Remote Similarity NPC178223
0.6667 Remote Similarity NPC477792
0.6667 Remote Similarity NPC89069
0.6667 Remote Similarity NPC85105
0.6667 Remote Similarity NPC131506
0.6667 Remote Similarity NPC478103
0.6667 Remote Similarity NPC277917
0.6667 Remote Similarity NPC166894
0.6667 Remote Similarity NPC195530
0.6667 Remote Similarity NPC149550
0.6622 Remote Similarity NPC472950
0.6622 Remote Similarity NPC317242
0.6622 Remote Similarity NPC158208
0.6622 Remote Similarity NPC243027
0.6622 Remote Similarity NPC3403
0.6622 Remote Similarity NPC196136
0.6622 Remote Similarity NPC472952
0.662 Remote Similarity NPC9942
0.6618 Remote Similarity NPC199937
0.6618 Remote Similarity NPC69149
0.6618 Remote Similarity NPC68656
0.6579 Remote Similarity NPC475725
0.6579 Remote Similarity NPC272841
0.6579 Remote Similarity NPC147993
0.6575 Remote Similarity NPC472341
0.6575 Remote Similarity NPC470610
0.6575 Remote Similarity NPC473238
0.6575 Remote Similarity NPC153719
0.6571 Remote Similarity NPC63190
0.6562 Remote Similarity NPC170780
0.6562 Remote Similarity NPC3025
0.6533 Remote Similarity NPC163597
0.6533 Remote Similarity NPC63958
0.6528 Remote Similarity NPC283316
0.6522 Remote Similarity NPC300442
0.6515 Remote Similarity NPC95958
0.65 Remote Similarity NPC127997
0.65 Remote Similarity NPC316035
0.65 Remote Similarity NPC95969
0.6486 Remote Similarity NPC477508
0.6486 Remote Similarity NPC48795
0.6479 Remote Similarity NPC478228
0.6447 Remote Similarity NPC302578
0.6447 Remote Similarity NPC185915
0.6447 Remote Similarity NPC64081
0.6447 Remote Similarity NPC472805
0.6447 Remote Similarity NPC128951
0.6447 Remote Similarity NPC169994
0.6447 Remote Similarity NPC475031
0.6447 Remote Similarity NPC476233
0.6447 Remote Similarity NPC90979
0.6447 Remote Similarity NPC474574
0.6447 Remote Similarity NPC105208
0.6447 Remote Similarity NPC477227
0.6447 Remote Similarity NPC192046
0.6438 Remote Similarity NPC471271
0.6438 Remote Similarity NPC471268

  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 NPC87296 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
0.7636 Intermediate Similarity NPD385 Approved
0.7636 Intermediate Similarity NPD384 Approved
0.6866 Remote Similarity NPD371 Approved
0.6857 Remote Similarity NPD4267 Clinical (unspecified phase)
0.6842 Remote Similarity NPD388 Approved
0.6842 Remote Similarity NPD386 Approved
0.6528 Remote Similarity NPD4787 Phase 1
0.6389 Remote Similarity NPD3699 Clinical (unspecified phase)
0.6389 Remote Similarity NPD3700 Clinical (unspecified phase)
0.6234 Remote Similarity NPD6116 Phase 1
0.6216 Remote Similarity NPD4808 Clinical (unspecified phase)
0.6216 Remote Similarity NPD4809 Clinical (unspecified phase)
0.6203 Remote Similarity NPD7525 Registered
0.6184 Remote Similarity NPD3703 Phase 2
0.6104 Remote Similarity NPD6117 Approved
0.6056 Remote Similarity NPD3171 Clinical (unspecified phase)
0.6053 Remote Similarity NPD6113 Clinical (unspecified phase)
0.6053 Remote Similarity NPD1810 Approved
0.6053 Remote Similarity NPD1811 Approved
0.5949 Remote Similarity NPD6115 Approved
0.5949 Remote Similarity NPD6114 Approved
0.5949 Remote Similarity NPD6118 Approved
0.5949 Remote Similarity NPD6697 Approved
0.5946 Remote Similarity NPD3698 Phase 2
0.5875 Remote Similarity NPD7645 Phase 2
0.5867 Remote Similarity NPD4245 Approved
0.5867 Remote Similarity NPD4244 Approved
0.5867 Remote Similarity NPD7532 Clinical (unspecified phase)
0.5811 Remote Similarity NPD5360 Phase 3
0.5811 Remote Similarity NPD5361 Clinical (unspecified phase)
0.5802 Remote Similarity NPD4748 Discontinued
0.5802 Remote Similarity NPD6928 Phase 2
0.5763 Remote Similarity NPD1462 Approved
0.575 Remote Similarity NPD3671 Phase 1
0.5696 Remote Similarity NPD3701 Clinical (unspecified phase)
0.569 Remote Similarity NPD1460 Approved
0.5667 Remote Similarity NPD367 Approved
0.5658 Remote Similarity NPD4789 Approved
0.5641 Remote Similarity NPD6926 Approved
0.5641 Remote Similarity NPD6924 Approved
0.5634 Remote Similarity NPD368 Approved
0.561 Remote Similarity NPD7509 Discontinued
0.56 Remote Similarity NPD6705 Phase 1

  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