Structure

Physi-Chem Properties

Molecular Weight:  317.27
Volume:  354.697
LogP:  4.631
LogD:  4.445
LogS:  -4.018
# Rotatable Bonds:  1
TPSA:  43.09
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  4
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.77
Synthetic Accessibility Score:  4.151
Fsp3:  0.952
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.735
MDCK Permeability:  1.0451413800183218e-05
Pgp-inhibitor:  0.981
Pgp-substrate:  0.057
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.012
30% Bioavailability (F30%):  0.853

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.129
Plasma Protein Binding (PPB):  77.56102752685547%
Volume Distribution (VD):  1.158
Pgp-substrate:  10.365387916564941%

ADMET: Metabolism

CYP1A2-inhibitor:  0.549
CYP1A2-substrate:  0.184
CYP2C19-inhibitor:  0.098
CYP2C19-substrate:  0.807
CYP2C9-inhibitor:  0.182
CYP2C9-substrate:  0.052
CYP2D6-inhibitor:  0.298
CYP2D6-substrate:  0.883
CYP3A4-inhibitor:  0.757
CYP3A4-substrate:  0.344

ADMET: Excretion

Clearance (CL):  22.611
Half-life (T1/2):  0.175

ADMET: Toxicity

hERG Blockers:  0.91
Human Hepatotoxicity (H-HT):  0.406
Drug-inuced Liver Injury (DILI):  0.896
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.618
Maximum Recommended Daily Dose:  0.447
Skin Sensitization:  0.959
Carcinogencity:  0.308
Eye Corrosion:  0.994
Eye Irritation:  0.16
Respiratory Toxicity:  0.966

Download Data

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

  Natural Product: NPC110615

Natural Product ID:  NPC110615
Common Name*:   1-((3R,5S,8R,9S,10S,13S,14S,17S)-3-Amino-10,13-Dimethylhexadecahydro-1H-Cyclopenta[A]Phenanthren-17-Yl)Ethanone
IUPAC Name:   1-[(3R,5S,8R,9S,10S,13S,14S,17S)-3-amino-10,13-dimethyl-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]ethanone
Synonyms:  
Standard InCHIKey:  POWBIOMTXFDIOP-SYBPFIFISA-N
Standard InCHI:  InChI=1S/C21H35NO/c1-13(23)17-6-7-18-16-5-4-14-12-15(22)8-10-20(14,2)19(16)9-11-21(17,18)3/h14-19H,4-12,22H2,1-3H3/p+1/t14-,15+,16-,17+,18-,19-,20-,21+/m0/s1
SMILES:  CC(=O)[C@H]1CC[C@H]2[C@@H]3CC[C@H]4C[C@@H](CC[C@]4(C)[C@H]3CC[C@]12C)[NH3+]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2322569
PubChem CID:   101702
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0003569] Pregnane 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
NPO26605 Funtumia elastica Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26605 Funtumia elastica Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10366 Vincetoxicum stauntonii Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10366 Vincetoxicum stauntonii Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26044 Melandrium firmum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO26605 Funtumia elastica Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10366 Vincetoxicum stauntonii Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26674 Leucas volkensii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24703 Prostanthera prunelloides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5175 Diplospora dubia Species Rubiaceae 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 Activity = 56.0 % PMID[541951]

☑ 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 NPC110615 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
0.8101 Intermediate Similarity NPC21667
0.7952 Intermediate Similarity NPC135005
0.7727 Intermediate Similarity NPC184819
0.7662 Intermediate Similarity NPC25110
0.7612 Intermediate Similarity NPC151464
0.7612 Intermediate Similarity NPC143597
0.7606 Intermediate Similarity NPC53276
0.75 Intermediate Similarity NPC469970
0.7471 Intermediate Similarity NPC476753
0.7471 Intermediate Similarity NPC476752
0.747 Intermediate Similarity NPC34811
0.7386 Intermediate Similarity NPC476754
0.7353 Intermediate Similarity NPC474105
0.7313 Intermediate Similarity NPC53245
0.7313 Intermediate Similarity NPC288296
0.7262 Intermediate Similarity NPC182106
0.7262 Intermediate Similarity NPC311769
0.7237 Intermediate Similarity NPC120167
0.7237 Intermediate Similarity NPC473442
0.72 Intermediate Similarity NPC271640
0.7111 Intermediate Similarity NPC174117
0.7042 Intermediate Similarity NPC21781
0.7011 Intermediate Similarity NPC259252
0.6883 Remote Similarity NPC245223
0.6842 Remote Similarity NPC58200
0.6735 Remote Similarity NPC476756
0.6735 Remote Similarity NPC244982
0.6714 Remote Similarity NPC307063
0.6711 Remote Similarity NPC39462
0.6711 Remote Similarity NPC189917
0.6711 Remote Similarity NPC168824
0.6711 Remote Similarity NPC107704
0.6711 Remote Similarity NPC96812
0.6711 Remote Similarity NPC43300
0.6705 Remote Similarity NPC43308
0.6667 Remote Similarity NPC312637
0.6667 Remote Similarity NPC124384
0.6618 Remote Similarity NPC274182
0.66 Remote Similarity NPC473994
0.6598 Remote Similarity NPC98765
0.6538 Remote Similarity NPC473225
0.6533 Remote Similarity NPC477740
0.6517 Remote Similarity NPC21035
0.6465 Remote Similarity NPC230677
0.6458 Remote Similarity NPC239768
0.6458 Remote Similarity NPC128698
0.6456 Remote Similarity NPC474962
0.6456 Remote Similarity NPC477857
0.6438 Remote Similarity NPC127798
0.6429 Remote Similarity NPC472828
0.6408 Remote Similarity NPC124358
0.6395 Remote Similarity NPC90150
0.6375 Remote Similarity NPC108131
0.6375 Remote Similarity NPC40574
0.6375 Remote Similarity NPC477856
0.6375 Remote Similarity NPC214770
0.6374 Remote Similarity NPC249312
0.6354 Remote Similarity NPC140685
0.6329 Remote Similarity NPC20610
0.6327 Remote Similarity NPC470592
0.6327 Remote Similarity NPC476755
0.6324 Remote Similarity NPC247786
0.6324 Remote Similarity NPC258672
0.6324 Remote Similarity NPC293343
0.63 Remote Similarity NPC195841
0.63 Remote Similarity NPC233256
0.6296 Remote Similarity NPC58057
0.6296 Remote Similarity NPC197701
0.6296 Remote Similarity NPC151018
0.6296 Remote Similarity NPC156277
0.6296 Remote Similarity NPC320549
0.6282 Remote Similarity NPC42060
0.625 Remote Similarity NPC182815
0.622 Remote Similarity NPC232112
0.622 Remote Similarity NPC474123
0.622 Remote Similarity NPC310766
0.6186 Remote Similarity NPC220111
0.6176 Remote Similarity NPC294440
0.6173 Remote Similarity NPC282593
0.6173 Remote Similarity NPC35734
0.6173 Remote Similarity NPC159577
0.6163 Remote Similarity NPC211322
0.6145 Remote Similarity NPC159497
0.6145 Remote Similarity NPC472854
0.6145 Remote Similarity NPC254340
0.6111 Remote Similarity NPC147513
0.6098 Remote Similarity NPC234707
0.6098 Remote Similarity NPC115023
0.6098 Remote Similarity NPC473267
0.6098 Remote Similarity NPC470078
0.6098 Remote Similarity NPC305501
0.6082 Remote Similarity NPC184033
0.6076 Remote Similarity NPC323005
0.6076 Remote Similarity NPC268736
0.6076 Remote Similarity NPC477931
0.6071 Remote Similarity NPC195155
0.6071 Remote Similarity NPC125767
0.6071 Remote Similarity NPC255650
0.6071 Remote Similarity NPC273366
0.6071 Remote Similarity NPC293803
0.6071 Remote Similarity NPC72444
0.6071 Remote Similarity NPC21220
0.6071 Remote Similarity NPC97534
0.6071 Remote Similarity NPC174964
0.6055 Remote Similarity NPC475340
0.6049 Remote Similarity NPC327728
0.6049 Remote Similarity NPC321732
0.6049 Remote Similarity NPC131892
0.6049 Remote Similarity NPC6120
0.6049 Remote Similarity NPC213178
0.6049 Remote Similarity NPC196197
0.6049 Remote Similarity NPC476734
0.6049 Remote Similarity NPC252032
0.6049 Remote Similarity NPC319671
0.6049 Remote Similarity NPC469941
0.6049 Remote Similarity NPC324607
0.6029 Remote Similarity NPC40249
0.6029 Remote Similarity NPC285814
0.6029 Remote Similarity NPC98246
0.6029 Remote Similarity NPC173996
0.6029 Remote Similarity NPC83187
0.6029 Remote Similarity NPC131981
0.6024 Remote Similarity NPC303613
0.6024 Remote Similarity NPC251705
0.6024 Remote Similarity NPC474228
0.6023 Remote Similarity NPC329782
0.6023 Remote Similarity NPC257962
0.6022 Remote Similarity NPC323156
0.6 Remote Similarity NPC474221
0.6 Remote Similarity NPC472487
0.6 Remote Similarity NPC34977
0.6 Remote Similarity NPC130459
0.6 Remote Similarity NPC246399
0.6 Remote Similarity NPC5767
0.6 Remote Similarity NPC478180
0.6 Remote Similarity NPC472486
0.6 Remote Similarity NPC475742
0.6 Remote Similarity NPC152718
0.5976 Remote Similarity NPC307176
0.5976 Remote Similarity NPC476731
0.5976 Remote Similarity NPC477929
0.5962 Remote Similarity NPC175585
0.5955 Remote Similarity NPC472312
0.5955 Remote Similarity NPC215474
0.5952 Remote Similarity NPC255021
0.5952 Remote Similarity NPC280026
0.5952 Remote Similarity NPC167702
0.593 Remote Similarity NPC264602
0.593 Remote Similarity NPC477918
0.593 Remote Similarity NPC475031
0.593 Remote Similarity NPC470557
0.593 Remote Similarity NPC23884
0.593 Remote Similarity NPC91665
0.593 Remote Similarity NPC221420
0.5918 Remote Similarity NPC473537
0.5918 Remote Similarity NPC292819
0.5909 Remote Similarity NPC12035
0.5904 Remote Similarity NPC126642
0.5904 Remote Similarity NPC469940
0.5904 Remote Similarity NPC223187
0.5904 Remote Similarity NPC472309
0.5904 Remote Similarity NPC89310
0.59 Remote Similarity NPC474001
0.5897 Remote Similarity NPC474027
0.5897 Remote Similarity NPC474435
0.5882 Remote Similarity NPC472311
0.5882 Remote Similarity NPC24014
0.5882 Remote Similarity NPC212733
0.5882 Remote Similarity NPC27349
0.587 Remote Similarity NPC157479
0.5862 Remote Similarity NPC478128
0.5862 Remote Similarity NPC185465
0.5862 Remote Similarity NPC63020
0.5859 Remote Similarity NPC252564
0.5859 Remote Similarity NPC475249
0.5854 Remote Similarity NPC64466
0.5854 Remote Similarity NPC139397
0.5844 Remote Similarity NPC270042
0.5843 Remote Similarity NPC118329
0.5843 Remote Similarity NPC109533
0.5843 Remote Similarity NPC152039
0.5842 Remote Similarity NPC226509
0.5833 Remote Similarity NPC52667
0.5833 Remote Similarity NPC470044
0.5833 Remote Similarity NPC470045
0.5814 Remote Similarity NPC4209
0.5814 Remote Similarity NPC471046
0.5814 Remote Similarity NPC69408
0.5802 Remote Similarity NPC20181
0.5802 Remote Similarity NPC220210
0.58 Remote Similarity NPC201712
0.5795 Remote Similarity NPC320144
0.5795 Remote Similarity NPC201459
0.5795 Remote Similarity NPC31302
0.5795 Remote Similarity NPC52951
0.5795 Remote Similarity NPC192744
0.5795 Remote Similarity NPC215843
0.5795 Remote Similarity NPC245029
0.5783 Remote Similarity NPC2634
0.5783 Remote Similarity NPC251929

  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 NPC110615 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
0.7692 Intermediate Similarity NPD4777 Suspended
0.7692 Intermediate Similarity NPD4776 Phase 2
0.7375 Intermediate Similarity NPD7155 Clinical (unspecified phase)
0.663 Remote Similarity NPD5769 Clinical (unspecified phase)
0.6538 Remote Similarity NPD5361 Clinical (unspecified phase)
0.6538 Remote Similarity NPD5360 Phase 3
0.6515 Remote Similarity NPD872 Approved
0.6515 Remote Similarity NPD874 Approved
0.6484 Remote Similarity NPD6934 Discontinued
0.6375 Remote Similarity NPD4789 Approved
0.6296 Remote Similarity NPD6081 Approved
0.6296 Remote Similarity NPD4808 Clinical (unspecified phase)
0.6296 Remote Similarity NPD4809 Clinical (unspecified phase)
0.6289 Remote Similarity NPD8418 Phase 2
0.6282 Remote Similarity NPD4224 Phase 2
0.6173 Remote Similarity NPD4244 Approved
0.6173 Remote Similarity NPD4245 Approved
0.6154 Remote Similarity NPD3171 Clinical (unspecified phase)
0.6139 Remote Similarity NPD6920 Discontinued
0.6098 Remote Similarity NPD4758 Discontinued
0.6098 Remote Similarity NPD5777 Approved
0.6049 Remote Similarity NPD3698 Phase 2
0.6049 Remote Similarity NPD3700 Clinical (unspecified phase)
0.6049 Remote Similarity NPD3699 Clinical (unspecified phase)
0.6029 Remote Similarity NPD344 Approved
0.6029 Remote Similarity NPD343 Approved
0.6029 Remote Similarity NPD345 Approved
0.6019 Remote Similarity NPD6415 Discontinued
0.5976 Remote Similarity NPD4747 Approved
0.597 Remote Similarity NPD871 Approved
0.597 Remote Similarity NPD873 Approved
0.5952 Remote Similarity NPD6113 Clinical (unspecified phase)
0.5926 Remote Similarity NPD3621 Clinical (unspecified phase)
0.5918 Remote Similarity NPD7919 Phase 3
0.5918 Remote Similarity NPD7920 Phase 3
0.5889 Remote Similarity NPD3527 Clinical (unspecified phase)
0.5875 Remote Similarity NPD375 Phase 2
0.587 Remote Similarity NPD8308 Discontinued
0.5862 Remote Similarity NPD5364 Discontinued
0.5859 Remote Similarity NPD8088 Phase 1
0.5854 Remote Similarity NPD4137 Phase 3
0.5814 Remote Similarity NPD6117 Approved
0.5783 Remote Similarity NPD4691 Approved
0.5765 Remote Similarity NPD5733 Approved
0.5747 Remote Similarity NPD6116 Phase 1
0.5698 Remote Similarity NPD3703 Phase 2
0.5682 Remote Similarity NPD6697 Approved
0.5682 Remote Similarity NPD6118 Approved
0.5682 Remote Similarity NPD6115 Approved
0.5682 Remote Similarity NPD6114 Approved
0.5616 Remote Similarity NPD3721 Approved
0.5616 Remote Similarity NPD3722 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