Structure

Physi-Chem Properties

Molecular Weight:  220.18
Volume:  248.481
LogP:  3.584
LogD:  4.255
LogS:  -4.5
# Rotatable Bonds:  1
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.672
Synthetic Accessibility Score:  4.648
Fsp3:  0.867
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:  -4.494
MDCK Permeability:  1.8152179109165445e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.18
30% Bioavailability (F30%):  0.012

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.856
Plasma Protein Binding (PPB):  66.51480865478516%
Volume Distribution (VD):  1.701
Pgp-substrate:  32.37516403198242%

ADMET: Metabolism

CYP1A2-inhibitor:  0.605
CYP1A2-substrate:  0.871
CYP2C19-inhibitor:  0.123
CYP2C19-substrate:  0.866
CYP2C9-inhibitor:  0.033
CYP2C9-substrate:  0.276
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.459
CYP3A4-inhibitor:  0.428
CYP3A4-substrate:  0.313

ADMET: Excretion

Clearance (CL):  8.146
Half-life (T1/2):  0.268

ADMET: Toxicity

hERG Blockers:  0.115
Human Hepatotoxicity (H-HT):  0.219
Drug-inuced Liver Injury (DILI):  0.347
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.041
Maximum Recommended Daily Dose:  0.02
Skin Sensitization:  0.783
Carcinogencity:  0.078
Eye Corrosion:  0.397
Eye Irritation:  0.869
Respiratory Toxicity:  0.697

Download Data

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

  Natural Product: NPC15152

Natural Product ID:  NPC15152
Common Name*:   RGLMWRGFUDRTOD-DXUDUQDWSA-N
IUPAC Name:   n.a.
Synonyms:   8Beta-Hydroxyprespatane
Standard InCHIKey:  RGLMWRGFUDRTOD-DXUDUQDWSA-N
Standard InCHI:  InChI=1S/C15H24O/c1-9(2)15(16)8-7-14(4)11-6-5-10(3)12(11)13(14)15/h10-13,16H,1,5-8H2,2-4H3/t10-,11+,12-,13+,14-,15+/m1/s1
SMILES:  C=C(C)[C@]1(CC[C@]2(C)[C@H]3CC[C@@H](C)[C@H]3[C@H]12)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL400116
PubChem CID:   23642709
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
NPO13916 Nephthea erecta Species Nephtheidae Eukaryota n.a. formosan soft coral n.a. PMID[17845002]
NPO13916 Nephthea erecta Species Nephtheidae Eukaryota n.a. Formosan soft coral n.a. PMID[24370010]
NPO13916 Nephthea erecta Species Nephtheidae Eukaryota n.a. n.a. n.a. PMID[9722490]
NPO13916 Nephthea erecta Species Nephtheidae 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
NPT139 Cell Line HT-29 Homo sapiens ED50 > 10.0 ug ml-1 PMID[565839]
NPT168 Cell Line P388 Mus musculus ED50 > 10.0 ug ml-1 PMID[565839]

☑ 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 NPC15152 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
0.9153 High Similarity NPC162109
0.8361 Intermediate Similarity NPC99480
0.8361 Intermediate Similarity NPC184049
0.8254 Intermediate Similarity NPC474480
0.8209 Intermediate Similarity NPC133873
0.8143 Intermediate Similarity NPC310643
0.803 Intermediate Similarity NPC308522
0.803 Intermediate Similarity NPC74885
0.7937 Intermediate Similarity NPC252809
0.7887 Intermediate Similarity NPC472472
0.7857 Intermediate Similarity NPC309178
0.7778 Intermediate Similarity NPC310228
0.7778 Intermediate Similarity NPC5698
0.7778 Intermediate Similarity NPC52431
0.7714 Intermediate Similarity NPC14352
0.7714 Intermediate Similarity NPC234527
0.7656 Intermediate Similarity NPC323153
0.7612 Intermediate Similarity NPC162309
0.7571 Intermediate Similarity NPC471660
0.7538 Intermediate Similarity NPC63111
0.7538 Intermediate Similarity NPC147524
0.7538 Intermediate Similarity NPC210346
0.75 Intermediate Similarity NPC136813
0.75 Intermediate Similarity NPC477791
0.75 Intermediate Similarity NPC469321
0.75 Intermediate Similarity NPC313185
0.75 Intermediate Similarity NPC472465
0.7463 Intermediate Similarity NPC477009
0.7463 Intermediate Similarity NPC238352
0.746 Intermediate Similarity NPC278550
0.7429 Intermediate Similarity NPC254845
0.7385 Intermediate Similarity NPC135648
0.7368 Intermediate Similarity NPC472471
0.7361 Intermediate Similarity NPC471659
0.7313 Intermediate Similarity NPC309300
0.7313 Intermediate Similarity NPC219940
0.726 Intermediate Similarity NPC201263
0.7258 Intermediate Similarity NPC286752
0.7237 Intermediate Similarity NPC80622
0.7206 Intermediate Similarity NPC261782
0.7206 Intermediate Similarity NPC469326
0.7206 Intermediate Similarity NPC205618
0.7162 Intermediate Similarity NPC471658
0.7162 Intermediate Similarity NPC126969
0.7143 Intermediate Similarity NPC167527
0.7143 Intermediate Similarity NPC224532
0.7101 Intermediate Similarity NPC469328
0.7083 Intermediate Similarity NPC164045
0.7031 Intermediate Similarity NPC39068
0.7031 Intermediate Similarity NPC264779
0.7018 Intermediate Similarity NPC474118
0.7018 Intermediate Similarity NPC51762
0.7015 Intermediate Similarity NPC41160
0.6986 Remote Similarity NPC472506
0.6962 Remote Similarity NPC260852
0.6962 Remote Similarity NPC472473
0.6957 Remote Similarity NPC300442
0.6957 Remote Similarity NPC19569
0.6912 Remote Similarity NPC474155
0.6912 Remote Similarity NPC473759
0.6892 Remote Similarity NPC476736
0.6885 Remote Similarity NPC131623
0.6875 Remote Similarity NPC277917
0.6875 Remote Similarity NPC178223
0.6875 Remote Similarity NPC89069
0.6875 Remote Similarity NPC283655
0.6875 Remote Similarity NPC166894
0.6866 Remote Similarity NPC234264
0.6866 Remote Similarity NPC47840
0.6857 Remote Similarity NPC475897
0.6849 Remote Similarity NPC41886
0.6849 Remote Similarity NPC471662
0.6825 Remote Similarity NPC192962
0.6818 Remote Similarity NPC474769
0.6818 Remote Similarity NPC189290
0.6806 Remote Similarity NPC144647
0.68 Remote Similarity NPC265921
0.68 Remote Similarity NPC85831
0.68 Remote Similarity NPC215215
0.6786 Remote Similarity NPC472466
0.6753 Remote Similarity NPC472501
0.6721 Remote Similarity NPC95969
0.6721 Remote Similarity NPC127997
0.6719 Remote Similarity NPC32222
0.6719 Remote Similarity NPC202146
0.6714 Remote Similarity NPC258595
0.6712 Remote Similarity NPC18543
0.6712 Remote Similarity NPC475728
0.6712 Remote Similarity NPC471781
0.6711 Remote Similarity NPC38141
0.6711 Remote Similarity NPC152017
0.6709 Remote Similarity NPC471661
0.6706 Remote Similarity NPC472468
0.6667 Remote Similarity NPC29976
0.6667 Remote Similarity NPC65786
0.6667 Remote Similarity NPC7491
0.6667 Remote Similarity NPC101285
0.6667 Remote Similarity NPC13789
0.6667 Remote Similarity NPC473614
0.6667 Remote Similarity NPC81615
0.6667 Remote Similarity NPC27853
0.6667 Remote Similarity NPC150713
0.6667 Remote Similarity NPC206875
0.6667 Remote Similarity NPC124112
0.6625 Remote Similarity NPC256750
0.6625 Remote Similarity NPC20262
0.6623 Remote Similarity NPC138502
0.6623 Remote Similarity NPC260301
0.6623 Remote Similarity NPC307336
0.662 Remote Similarity NPC279434
0.662 Remote Similarity NPC476406
0.6618 Remote Similarity NPC40206
0.6615 Remote Similarity NPC45387
0.6582 Remote Similarity NPC472470
0.6579 Remote Similarity NPC23231
0.6579 Remote Similarity NPC251435
0.6579 Remote Similarity NPC77501
0.6579 Remote Similarity NPC185536
0.6579 Remote Similarity NPC60818
0.6575 Remote Similarity NPC474900
0.6575 Remote Similarity NPC90115
0.6575 Remote Similarity NPC217570
0.6575 Remote Similarity NPC474248
0.6571 Remote Similarity NPC68656
0.6571 Remote Similarity NPC107540
0.6571 Remote Similarity NPC140233
0.6571 Remote Similarity NPC287744
0.6571 Remote Similarity NPC475704
0.6557 Remote Similarity NPC100445
0.6552 Remote Similarity NPC472467
0.6543 Remote Similarity NPC471340
0.6538 Remote Similarity NPC301707
0.6538 Remote Similarity NPC472342
0.6538 Remote Similarity NPC477514
0.6538 Remote Similarity NPC472502
0.6538 Remote Similarity NPC42853
0.6538 Remote Similarity NPC470944
0.6538 Remote Similarity NPC472499
0.6538 Remote Similarity NPC475
0.6538 Remote Similarity NPC472500
0.6533 Remote Similarity NPC310608
0.6533 Remote Similarity NPC329763
0.6528 Remote Similarity NPC161612
0.6528 Remote Similarity NPC171225
0.6528 Remote Similarity NPC33583
0.6515 Remote Similarity NPC3025
0.6515 Remote Similarity NPC274396
0.6515 Remote Similarity NPC24443
0.6515 Remote Similarity NPC179024
0.65 Remote Similarity NPC87439
0.6494 Remote Similarity NPC247325
0.6494 Remote Similarity NPC244488
0.6494 Remote Similarity NPC476317
0.6479 Remote Similarity NPC476737
0.6479 Remote Similarity NPC27243
0.6463 Remote Similarity NPC242016
0.6463 Remote Similarity NPC116613
0.6456 Remote Similarity NPC32758
0.6456 Remote Similarity NPC49627
0.6456 Remote Similarity NPC24504
0.6456 Remote Similarity NPC5604
0.6456 Remote Similarity NPC49599
0.6456 Remote Similarity NPC301769
0.6456 Remote Similarity NPC476316
0.6447 Remote Similarity NPC27395
0.6447 Remote Similarity NPC469593
0.6447 Remote Similarity NPC469533
0.6447 Remote Similarity NPC474524
0.6447 Remote Similarity NPC329090
0.6447 Remote Similarity NPC469534
0.6447 Remote Similarity NPC475517
0.6441 Remote Similarity NPC166362
0.6441 Remote Similarity NPC15162
0.6441 Remote Similarity NPC141777
0.6441 Remote Similarity NPC227670
0.6438 Remote Similarity NPC160209
0.6438 Remote Similarity NPC276616
0.6438 Remote Similarity NPC245795
0.6429 Remote Similarity NPC174956
0.6429 Remote Similarity NPC211291
0.6429 Remote Similarity NPC133368
0.6429 Remote Similarity NPC50435
0.6418 Remote Similarity NPC291147
0.641 Remote Similarity NPC137547
0.641 Remote Similarity NPC212241
0.641 Remote Similarity NPC257191
0.641 Remote Similarity NPC331618
0.641 Remote Similarity NPC119355
0.641 Remote Similarity NPC248830
0.6406 Remote Similarity NPC35519
0.6406 Remote Similarity NPC181255
0.6406 Remote Similarity NPC157781
0.6406 Remote Similarity NPC306195
0.6406 Remote Similarity NPC179169
0.64 Remote Similarity NPC111234
0.64 Remote Similarity NPC469737
0.64 Remote Similarity NPC469343
0.6389 Remote Similarity NPC230107
0.6389 Remote Similarity NPC473929
0.6389 Remote Similarity NPC135650

  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 NPC15152 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
0.7083 Intermediate Similarity NPD4243 Approved
0.6892 Remote Similarity NPD4785 Approved
0.6892 Remote Similarity NPD4784 Approved
0.68 Remote Similarity NPD4190 Phase 3
0.68 Remote Similarity NPD5275 Approved
0.6456 Remote Similarity NPD4195 Approved
0.6447 Remote Similarity NPD6924 Approved
0.6447 Remote Similarity NPD6926 Approved
0.6375 Remote Similarity NPD6931 Approved
0.6375 Remote Similarity NPD6930 Phase 2
0.6282 Remote Similarity NPD6933 Approved
0.6282 Remote Similarity NPD3701 Clinical (unspecified phase)
0.625 Remote Similarity NPD6929 Approved
0.6235 Remote Similarity NPD4751 Clinical (unspecified phase)
0.622 Remote Similarity NPD4221 Approved
0.622 Remote Similarity NPD4223 Phase 3
0.6154 Remote Similarity NPD6942 Approved
0.6154 Remote Similarity NPD7339 Approved
0.6145 Remote Similarity NPD4788 Approved
0.6145 Remote Similarity NPD5331 Approved
0.6145 Remote Similarity NPD5332 Approved
0.6145 Remote Similarity NPD6695 Phase 3
0.6133 Remote Similarity NPD6922 Approved
0.6133 Remote Similarity NPD6923 Approved
0.6098 Remote Similarity NPD4790 Discontinued
0.6071 Remote Similarity NPD4197 Approved
0.6071 Remote Similarity NPD7338 Clinical (unspecified phase)
0.6053 Remote Similarity NPD7143 Approved
0.6053 Remote Similarity NPD7144 Approved
0.6 Remote Similarity NPD5776 Phase 2
0.6 Remote Similarity NPD6893 Approved
0.6 Remote Similarity NPD5329 Approved
0.6 Remote Similarity NPD6925 Approved
0.5976 Remote Similarity NPD7514 Phase 3
0.5976 Remote Similarity NPD7525 Registered
0.5976 Remote Similarity NPD4748 Discontinued
0.5974 Remote Similarity NPD7150 Approved
0.5974 Remote Similarity NPD7152 Approved
0.5974 Remote Similarity NPD7151 Approved
0.5952 Remote Similarity NPD5362 Discontinued
0.593 Remote Similarity NPD4138 Approved
0.593 Remote Similarity NPD4688 Approved
0.593 Remote Similarity NPD4689 Approved
0.593 Remote Similarity NPD4693 Phase 3
0.593 Remote Similarity NPD5205 Approved
0.593 Remote Similarity NPD5280 Approved
0.593 Remote Similarity NPD4690 Approved
0.593 Remote Similarity NPD4694 Approved
0.593 Remote Similarity NPD5690 Phase 2
0.5926 Remote Similarity NPD7322 Clinical (unspecified phase)
0.5926 Remote Similarity NPD7145 Approved
0.5904 Remote Similarity NPD4139 Approved
0.5904 Remote Similarity NPD4692 Approved
0.5882 Remote Similarity NPD342 Phase 1
0.5862 Remote Similarity NPD7750 Discontinued
0.5862 Remote Similarity NPD7524 Approved
0.5833 Remote Similarity NPD368 Approved
0.5814 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5802 Remote Similarity NPD6932 Approved
0.5795 Remote Similarity NPD4722 Approved
0.5795 Remote Similarity NPD4723 Approved
0.5795 Remote Similarity NPD4518 Approved
0.5783 Remote Similarity NPD7332 Phase 2
0.5783 Remote Similarity NPD7509 Discontinued
0.5783 Remote Similarity NPD4819 Approved
0.5783 Remote Similarity NPD4820 Approved
0.5783 Remote Similarity NPD4821 Approved
0.5783 Remote Similarity NPD4822 Approved
0.5732 Remote Similarity NPD5784 Clinical (unspecified phase)
0.573 Remote Similarity NPD4753 Phase 2
0.5714 Remote Similarity NPD6902 Approved
0.5714 Remote Similarity NPD6898 Phase 1
0.5698 Remote Similarity NPD3133 Approved
0.5698 Remote Similarity NPD3666 Approved
0.5698 Remote Similarity NPD3665 Phase 1
0.5667 Remote Similarity NPD4096 Approved
0.5667 Remote Similarity NPD4001 Clinical (unspecified phase)
0.5663 Remote Similarity NPD6683 Phase 2
0.5604 Remote Similarity NPD5284 Approved
0.5604 Remote Similarity NPD7087 Discontinued
0.5604 Remote Similarity NPD5281 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