Structure

Physi-Chem Properties

Molecular Weight:  378.33
Volume:  448.072
LogP:  7.357
LogD:  5.65
LogS:  -7.432
# Rotatable Bonds:  4
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.432
Synthetic Accessibility Score:  4.889
Fsp3:  0.714
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.056
MDCK Permeability:  1.2713628166238777e-05
Pgp-inhibitor:  0.999
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.99
30% Bioavailability (F30%):  0.956

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.012
Plasma Protein Binding (PPB):  92.52201080322266%
Volume Distribution (VD):  2.556
Pgp-substrate:  1.7509874105453491%

ADMET: Metabolism

CYP1A2-inhibitor:  0.113
CYP1A2-substrate:  0.729
CYP2C19-inhibitor:  0.306
CYP2C19-substrate:  0.969
CYP2C9-inhibitor:  0.324
CYP2C9-substrate:  0.185
CYP2D6-inhibitor:  0.797
CYP2D6-substrate:  0.632
CYP3A4-inhibitor:  0.882
CYP3A4-substrate:  0.922

ADMET: Excretion

Clearance (CL):  1.208
Half-life (T1/2):  0.103

ADMET: Toxicity

hERG Blockers:  0.646
Human Hepatotoxicity (H-HT):  0.399
Drug-inuced Liver Injury (DILI):  0.069
AMES Toxicity:  0.013
Rat Oral Acute Toxicity:  0.668
Maximum Recommended Daily Dose:  0.969
Skin Sensitization:  0.966
Carcinogencity:  0.016
Eye Corrosion:  0.007
Eye Irritation:  0.113
Respiratory Toxicity:  0.941

Download Data

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

  Natural Product: NPC470893

Natural Product ID:  NPC470893
Common Name*:   Ergosta-4,6,8(14),22-Tetraen-3-One
IUPAC Name:   (9R,10R,13R,17R)-17-[(E,2R,5R)-5,6-dimethylhept-3-en-2-yl]-10,13-dimethyl-2,3,9,11,12,15,16,17-octahydro-1H-cyclopenta[a]phenanthrene
Synonyms:  
Standard InCHIKey:  AITSBSNXXNIPSL-PDNGUNMXSA-N
Standard InCHI:  InChI=1S/C28H42/c1-19(2)20(3)10-11-21(4)24-14-15-25-23-13-12-22-9-7-8-17-27(22,5)26(23)16-18-28(24,25)6/h9-13,19-21,24,26H,7-8,14-18H2,1-6H3/b11-10+/t20-,21+,24+,26-,27-,28+/m0/s1
SMILES:  CC([C@H](/C=C/[C@H]([C@H]1CCC2=C3[C@H](CC[C@]12C)[C@@]1(C)CCCC=C1C=C3)C)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL229618
PubChem CID:   44424395
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0003567] Ergostane steroids

*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
NPO30573 Antrodia camphorata Species Fomitopsidaceae Eukaryota n.a. n.a. n.a. PMID[14738384]
NPO30573 Antrodia camphorata Species Fomitopsidaceae Eukaryota fruiting bodies n.a. n.a. PMID[16643055]
NPO30573 Antrodia camphorata Species Fomitopsidaceae Eukaryota n.a. n.a. n.a. PMID[17559265]
NPO30573 Antrodia camphorata Species Fomitopsidaceae Eukaryota n.a. n.a. n.a. PMID[24387703]
NPO15599 Daldinia concentrica Species n.a. Eukaryota Fruiting Bodies n.a. n.a. PMID[29715021]
NPO30573 Antrodia camphorata Species Fomitopsidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15599 Daldinia concentrica Species n.a. Eukaryota n.a. n.a. n.a. Database[Title]
NPO15599 Daldinia concentrica Species n.a. 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
NPT2 Others Unspecified IC50 > 100000.0 nM PMID[450697]

☑ 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 NPC470893 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
0.9091 High Similarity NPC469769
0.8462 Intermediate Similarity NPC17810
0.8214 Intermediate Similarity NPC123194
0.8077 Intermediate Similarity NPC323445
0.7885 Intermediate Similarity NPC49088
0.7778 Intermediate Similarity NPC17518
0.7727 Intermediate Similarity NPC181204
0.7647 Intermediate Similarity NPC177470
0.7593 Intermediate Similarity NPC124851
0.7547 Intermediate Similarity NPC86683
0.7455 Intermediate Similarity NPC22765
0.7451 Intermediate Similarity NPC144023
0.7358 Intermediate Similarity NPC202189
0.7321 Intermediate Similarity NPC200129
0.7302 Intermediate Similarity NPC474086
0.7288 Intermediate Similarity NPC469770
0.7255 Intermediate Similarity NPC183670
0.7206 Intermediate Similarity NPC470078
0.7143 Intermediate Similarity NPC471468
0.7121 Intermediate Similarity NPC176107
0.7097 Intermediate Similarity NPC475716
0.7037 Intermediate Similarity NPC248411
0.697 Remote Similarity NPC92327
0.6964 Remote Similarity NPC178644
0.6949 Remote Similarity NPC127944
0.6912 Remote Similarity NPC182815
0.6909 Remote Similarity NPC13991
0.6909 Remote Similarity NPC114239
0.6909 Remote Similarity NPC296337
0.6909 Remote Similarity NPC241784
0.6875 Remote Similarity NPC469728
0.6863 Remote Similarity NPC48638
0.6863 Remote Similarity NPC266298
0.6863 Remote Similarity NPC45727
0.6863 Remote Similarity NPC239039
0.6857 Remote Similarity NPC470045
0.6857 Remote Similarity NPC470044
0.6852 Remote Similarity NPC192529
0.6812 Remote Similarity NPC475728
0.6812 Remote Similarity NPC9161
0.6812 Remote Similarity NPC49422
0.6792 Remote Similarity NPC120926
0.6792 Remote Similarity NPC218918
0.6774 Remote Similarity NPC475696
0.6774 Remote Similarity NPC474415
0.6774 Remote Similarity NPC474528
0.6765 Remote Similarity NPC216460
0.6765 Remote Similarity NPC20610
0.6719 Remote Similarity NPC176621
0.6716 Remote Similarity NPC323005
0.6716 Remote Similarity NPC176171
0.6714 Remote Similarity NPC115023
0.6667 Remote Similarity NPC269877
0.6667 Remote Similarity NPC105246
0.6667 Remote Similarity NPC167272
0.6667 Remote Similarity NPC4638
0.6667 Remote Similarity NPC473171
0.6667 Remote Similarity NPC190232
0.6667 Remote Similarity NPC473912
0.6667 Remote Similarity NPC476679
0.6622 Remote Similarity NPC76931
0.6622 Remote Similarity NPC307965
0.6622 Remote Similarity NPC18603
0.6622 Remote Similarity NPC186191
0.6622 Remote Similarity NPC205455
0.662 Remote Similarity NPC251705
0.6618 Remote Similarity NPC193770
0.6613 Remote Similarity NPC55412
0.6613 Remote Similarity NPC249645
0.6604 Remote Similarity NPC246165
0.6575 Remote Similarity NPC470362
0.6571 Remote Similarity NPC159577
0.6571 Remote Similarity NPC282593
0.6571 Remote Similarity NPC35734
0.6567 Remote Similarity NPC163678
0.6562 Remote Similarity NPC474455
0.6562 Remote Similarity NPC474454
0.6562 Remote Similarity NPC474420
0.6545 Remote Similarity NPC166362
0.6545 Remote Similarity NPC86538
0.6545 Remote Similarity NPC141777
0.6545 Remote Similarity NPC60556
0.6545 Remote Similarity NPC227670
0.6545 Remote Similarity NPC109813
0.6538 Remote Similarity NPC297643
0.6538 Remote Similarity NPC229262
0.6538 Remote Similarity NPC139717
0.6533 Remote Similarity NPC170793
0.6528 Remote Similarity NPC474797
0.6528 Remote Similarity NPC309852
0.6528 Remote Similarity NPC474796
0.6528 Remote Similarity NPC329866
0.6522 Remote Similarity NPC32055
0.6522 Remote Similarity NPC87141
0.6522 Remote Similarity NPC310992
0.6515 Remote Similarity NPC197238
0.6515 Remote Similarity NPC202118
0.6508 Remote Similarity NPC321568
0.6508 Remote Similarity NPC281986
0.6508 Remote Similarity NPC474457
0.6508 Remote Similarity NPC208749
0.6508 Remote Similarity NPC22019
0.6508 Remote Similarity NPC230823
0.6486 Remote Similarity NPC475027
0.6481 Remote Similarity NPC103290
0.6479 Remote Similarity NPC234707
0.6479 Remote Similarity NPC54123
0.6479 Remote Similarity NPC21773
0.6471 Remote Similarity NPC222366
0.6471 Remote Similarity NPC149680
0.6471 Remote Similarity NPC286669
0.6471 Remote Similarity NPC92224
0.6471 Remote Similarity NPC476039
0.6471 Remote Similarity NPC282119
0.6462 Remote Similarity NPC323153
0.6438 Remote Similarity NPC293803
0.6438 Remote Similarity NPC125828
0.6429 Remote Similarity NPC139397
0.6429 Remote Similarity NPC256846
0.6418 Remote Similarity NPC469662
0.641 Remote Similarity NPC470384
0.6406 Remote Similarity NPC60772
0.64 Remote Similarity NPC318136
0.6393 Remote Similarity NPC295777
0.6393 Remote Similarity NPC69898
0.6389 Remote Similarity NPC474228
0.6389 Remote Similarity NPC303613
0.6377 Remote Similarity NPC197805
0.6377 Remote Similarity NPC45782
0.6364 Remote Similarity NPC4166
0.6364 Remote Similarity NPC193180
0.6351 Remote Similarity NPC113733
0.6351 Remote Similarity NPC134330
0.6351 Remote Similarity NPC46160
0.6351 Remote Similarity NPC292589
0.6351 Remote Similarity NPC129165
0.6351 Remote Similarity NPC69408
0.6351 Remote Similarity NPC474463
0.6351 Remote Similarity NPC202642
0.6346 Remote Similarity NPC76145
0.6346 Remote Similarity NPC190810
0.6346 Remote Similarity NPC34764
0.6338 Remote Similarity NPC307176
0.6338 Remote Similarity NPC251929
0.6338 Remote Similarity NPC40574
0.6338 Remote Similarity NPC477856
0.6338 Remote Similarity NPC260040
0.6338 Remote Similarity NPC265782
0.6338 Remote Similarity NPC2634
0.6338 Remote Similarity NPC214770
0.6329 Remote Similarity NPC231310
0.6329 Remote Similarity NPC238485
0.6324 Remote Similarity NPC268039
0.6316 Remote Similarity NPC229403
0.6308 Remote Similarity NPC5698
0.6308 Remote Similarity NPC309825
0.6301 Remote Similarity NPC476904
0.6301 Remote Similarity NPC329090
0.6301 Remote Similarity NPC27395
0.6296 Remote Similarity NPC78551
0.6296 Remote Similarity NPC287079
0.6296 Remote Similarity NPC62086
0.6296 Remote Similarity NPC227632
0.6286 Remote Similarity NPC260474
0.6286 Remote Similarity NPC188292
0.6286 Remote Similarity NPC160209
0.6282 Remote Similarity NPC202389
0.6282 Remote Similarity NPC201852
0.6282 Remote Similarity NPC311092
0.6267 Remote Similarity NPC475025
0.6267 Remote Similarity NPC214570
0.625 Remote Similarity NPC11130
0.625 Remote Similarity NPC267626
0.625 Remote Similarity NPC265789
0.625 Remote Similarity NPC49575
0.625 Remote Similarity NPC90803
0.625 Remote Similarity NPC23145
0.625 Remote Similarity NPC474118
0.625 Remote Similarity NPC51762
0.625 Remote Similarity NPC90506
0.625 Remote Similarity NPC55004
0.625 Remote Similarity NPC5701
0.625 Remote Similarity NPC305501
0.6232 Remote Similarity NPC279434
0.623 Remote Similarity NPC473728
0.6216 Remote Similarity NPC230301
0.6216 Remote Similarity NPC322353
0.6216 Remote Similarity NPC171148
0.6216 Remote Similarity NPC313179
0.6216 Remote Similarity NPC288035
0.6216 Remote Similarity NPC471723
0.6216 Remote Similarity NPC121744
0.6216 Remote Similarity NPC141071
0.6216 Remote Similarity NPC22105
0.6216 Remote Similarity NPC304309
0.6216 Remote Similarity NPC69383
0.6216 Remote Similarity NPC257347
0.6216 Remote Similarity NPC136188
0.6216 Remote Similarity NPC118508
0.6216 Remote Similarity NPC134847

  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 NPC470893 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
0.8462 Intermediate Similarity NPD8262 Approved
0.7 Intermediate Similarity NPD5733 Approved
0.7 Intermediate Similarity NPD4687 Approved
0.6957 Remote Similarity NPD5276 Approved
0.6812 Remote Similarity NPD7144 Approved
0.6812 Remote Similarity NPD7143 Approved
0.6761 Remote Similarity NPD4058 Approved
0.6714 Remote Similarity NPD7152 Approved
0.6714 Remote Similarity NPD7151 Approved
0.6714 Remote Similarity NPD7150 Approved
0.6667 Remote Similarity NPD6922 Approved
0.6667 Remote Similarity NPD6923 Approved
0.6667 Remote Similarity NPD1799 Clinical (unspecified phase)
0.6613 Remote Similarity NPD4219 Approved
0.6571 Remote Similarity NPD6939 Phase 2
0.6571 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6528 Remote Similarity NPD4784 Approved
0.6528 Remote Similarity NPD4785 Approved
0.6522 Remote Similarity NPD3621 Clinical (unspecified phase)
0.6479 Remote Similarity NPD4243 Approved
0.6429 Remote Similarity NPD4137 Phase 3
0.6346 Remote Similarity NPD319 Phase 1
0.6338 Remote Similarity NPD4747 Approved
0.6338 Remote Similarity NPD4691 Approved
0.6301 Remote Similarity NPD6926 Approved
0.6301 Remote Similarity NPD6924 Approved
0.6267 Remote Similarity NPD6932 Approved
0.6216 Remote Similarity NPD6942 Approved
0.6216 Remote Similarity NPD7339 Approved
0.6216 Remote Similarity NPD8264 Approved
0.6203 Remote Similarity NPD3527 Clinical (unspecified phase)
0.6184 Remote Similarity NPD7145 Approved
0.6176 Remote Similarity NPD5325 Clinical (unspecified phase)
0.6133 Remote Similarity NPD6933 Approved
0.6119 Remote Similarity NPD4192 Approved
0.6119 Remote Similarity NPD4193 Approved
0.6119 Remote Similarity NPD4191 Approved
0.6119 Remote Similarity NPD4194 Approved
0.6053 Remote Similarity NPD5776 Phase 2
0.6053 Remote Similarity NPD6925 Approved
0.6026 Remote Similarity NPD7514 Phase 3
0.6024 Remote Similarity NPD4518 Approved
0.6 Remote Similarity NPD4190 Phase 3
0.6 Remote Similarity NPD5275 Approved
0.5974 Remote Similarity NPD7322 Clinical (unspecified phase)
0.5949 Remote Similarity NPD6902 Approved
0.5921 Remote Similarity NPD3701 Clinical (unspecified phase)
0.5897 Remote Similarity NPD4195 Approved
0.5897 Remote Similarity NPD6929 Approved
0.5897 Remote Similarity NPD6683 Phase 2
0.5882 Remote Similarity NPD4001 Clinical (unspecified phase)
0.5823 Remote Similarity NPD6930 Phase 2
0.5823 Remote Similarity NPD6931 Approved
0.5823 Remote Similarity NPD7332 Phase 2
0.5783 Remote Similarity NPD5280 Approved
0.5783 Remote Similarity NPD5279 Phase 3
0.5783 Remote Similarity NPD4694 Approved
0.5698 Remote Similarity NPD5207 Approved
0.5632 Remote Similarity NPD5281 Approved
0.5632 Remote Similarity NPD5694 Approved
0.5632 Remote Similarity NPD5284 Approved
0.5632 Remote Similarity NPD6050 Approved
0.5625 Remote Similarity NPD7525 Registered
0.5625 Remote Similarity NPD7509 Discontinued
0.561 Remote Similarity NPD6695 Phase 3

  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