Structure

Physi-Chem Properties

Molecular Weight:  358.33
Volume:  408.791
LogP:  5.475
LogD:  4.329
LogS:  -3.037
# Rotatable Bonds:  3
TPSA:  15.27
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.706
Synthetic Accessibility Score:  4.501
Fsp3:  0.917
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:  -4.915
MDCK Permeability:  8.37899642647244e-06
Pgp-inhibitor:  0.973
Pgp-substrate:  0.484
Human Intestinal Absorption (HIA):  0.021
20% Bioavailability (F20%):  0.045
30% Bioavailability (F30%):  0.054

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.717
Plasma Protein Binding (PPB):  56.975833892822266%
Volume Distribution (VD):  1.131
Pgp-substrate:  47.89179992675781%

ADMET: Metabolism

CYP1A2-inhibitor:  0.106
CYP1A2-substrate:  0.368
CYP2C19-inhibitor:  0.063
CYP2C19-substrate:  0.951
CYP2C9-inhibitor:  0.043
CYP2C9-substrate:  0.05
CYP2D6-inhibitor:  0.773
CYP2D6-substrate:  0.909
CYP3A4-inhibitor:  0.893
CYP3A4-substrate:  0.707

ADMET: Excretion

Clearance (CL):  17.342
Half-life (T1/2):  0.038

ADMET: Toxicity

hERG Blockers:  0.263
Human Hepatotoxicity (H-HT):  0.508
Drug-inuced Liver Injury (DILI):  0.353
AMES Toxicity:  0.032
Rat Oral Acute Toxicity:  0.825
Maximum Recommended Daily Dose:  0.948
Skin Sensitization:  0.944
Carcinogencity:  0.826
Eye Corrosion:  0.056
Eye Irritation:  0.015
Respiratory Toxicity:  0.98

Download Data

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

  Natural Product: NPC211322

Natural Product ID:  NPC211322
Common Name*:   [17-(1-Dimethylamino-Ethyl)-10,13-Dimethyl-2,3,4,5,6,7,8,9,10,11,12,13,14,15-Tetradecahydro-1H-Cyclopenta[A]Phenanthren-3-Yl]-Methyl-Amine
IUPAC Name:   (3S,5S,8R,9S,10S,13S,14S)-17-[(1S)-1-(dimethylamino)ethyl]-N,10,13-trimethyl-2,3,4,5,6,7,8,9,11,12,14,15-dodecahydro-1H-cyclopenta[a]phenanthren-3-amine
Synonyms:  
Standard InCHIKey:  ODQOCJVSQCAFKC-GSTPBQSSSA-N
Standard InCHI:  InChI=1S/C24H42N2/c1-16(26(5)6)20-9-10-21-19-8-7-17-15-18(25-4)11-13-23(17,2)22(19)12-14-24(20,21)3/h9,16-19,21-22,25H,7-8,10-15H2,1-6H3/t16-,17-,18-,19-,21-,22-,23-,24+/m0/s1
SMILES:  C[C@@H](C1=CC[C@H]2[C@@H]3CC[C@H]4C[C@H](CC[C@]4(C)[C@H]3CC[C@]12C)NC)N(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL137721
PubChem CID:   11268352
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0002340] Azasteroids and derivatives

*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
NPO27888 Sarcococca saligna Species Buxaceae Eukaryota n.a. n.a. n.a. PMID[14584959]
NPO27888 Sarcococca saligna Species Buxaceae Eukaryota n.a. n.a. n.a. PMID[14643329]
NPO27888 Sarcococca saligna Species Buxaceae Eukaryota n.a. n.a. n.a. PMID[9548847]
NPO27888 Sarcococca saligna Species Buxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27888 Sarcococca saligna Species Buxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27888 Sarcococca saligna Species Buxaceae 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
NPT204 Individual Protein Acetylcholinesterase Homo sapiens IC50 = 20417.38 nM PMID[491471]

☑ 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 NPC211322 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
0.8861 High Similarity NPC472312
0.8784 High Similarity NPC265789
0.8734 High Similarity NPC152039
0.8734 High Similarity NPC118329
0.8734 High Similarity NPC329782
0.8608 High Similarity NPC12035
0.8553 High Similarity NPC476904
0.8533 High Similarity NPC21773
0.8272 Intermediate Similarity NPC474122
0.8101 Intermediate Similarity NPC7214
0.8095 Intermediate Similarity NPC24733
0.8 Intermediate Similarity NPC157479
0.7973 Intermediate Similarity NPC469970
0.7907 Intermediate Similarity NPC43308
0.7857 Intermediate Similarity NPC171639
0.7838 Intermediate Similarity NPC53276
0.775 Intermediate Similarity NPC125828
0.7738 Intermediate Similarity NPC283277
0.7674 Intermediate Similarity NPC147513
0.7662 Intermediate Similarity NPC271640
0.764 Intermediate Similarity NPC84171
0.7582 Intermediate Similarity NPC476754
0.7529 Intermediate Similarity NPC215474
0.7471 Intermediate Similarity NPC152684
0.7396 Intermediate Similarity NPC58200
0.7386 Intermediate Similarity NPC166458
0.7333 Intermediate Similarity NPC219621
0.7297 Intermediate Similarity NPC21781
0.7283 Intermediate Similarity NPC476753
0.7283 Intermediate Similarity NPC476752
0.7241 Intermediate Similarity NPC21667
0.7229 Intermediate Similarity NPC174803
0.7229 Intermediate Similarity NPC259989
0.7209 Intermediate Similarity NPC90150
0.7079 Intermediate Similarity NPC311769
0.7079 Intermediate Similarity NPC182106
0.7024 Intermediate Similarity NPC25110
0.7013 Intermediate Similarity NPC472544
0.7011 Intermediate Similarity NPC257962
0.701 Intermediate Similarity NPC135799
0.6979 Remote Similarity NPC167419
0.6974 Remote Similarity NPC317778
0.6962 Remote Similarity NPC37792
0.6889 Remote Similarity NPC75810
0.6863 Remote Similarity NPC159367
0.6848 Remote Similarity NPC259252
0.6804 Remote Similarity NPC474164
0.6768 Remote Similarity NPC118275
0.6737 Remote Similarity NPC93027
0.6731 Remote Similarity NPC472313
0.6711 Remote Similarity NPC324944
0.6707 Remote Similarity NPC138409
0.6707 Remote Similarity NPC184919
0.6701 Remote Similarity NPC476903
0.6667 Remote Similarity NPC230677
0.6667 Remote Similarity NPC55462
0.663 Remote Similarity NPC56107
0.6628 Remote Similarity NPC476308
0.6623 Remote Similarity NPC472827
0.6604 Remote Similarity NPC474452
0.66 Remote Similarity NPC474582
0.6579 Remote Similarity NPC173815
0.6566 Remote Similarity NPC140685
0.6548 Remote Similarity NPC476329
0.6535 Remote Similarity NPC176012
0.6509 Remote Similarity NPC474459
0.6509 Remote Similarity NPC79238
0.6506 Remote Similarity NPC245223
0.6506 Remote Similarity NPC124384
0.6505 Remote Similarity NPC233256
0.6505 Remote Similarity NPC195841
0.6505 Remote Similarity NPC474695
0.6494 Remote Similarity NPC472830
0.6465 Remote Similarity NPC140300
0.6447 Remote Similarity NPC318036
0.6429 Remote Similarity NPC120167
0.6429 Remote Similarity NPC473442
0.6413 Remote Similarity NPC471867
0.6373 Remote Similarity NPC226509
0.6373 Remote Similarity NPC247060
0.6364 Remote Similarity NPC474457
0.6296 Remote Similarity NPC80834
0.6296 Remote Similarity NPC469968
0.6286 Remote Similarity NPC476756
0.6286 Remote Similarity NPC244982
0.6263 Remote Similarity NPC272732
0.6263 Remote Similarity NPC311164
0.6262 Remote Similarity NPC472359
0.6214 Remote Similarity NPC50815
0.6214 Remote Similarity NPC471083
0.6214 Remote Similarity NPC152718
0.6207 Remote Similarity NPC237286
0.6203 Remote Similarity NPC474455
0.6203 Remote Similarity NPC474420
0.6203 Remote Similarity NPC474454
0.6196 Remote Similarity NPC471868
0.6176 Remote Similarity NPC275686
0.6173 Remote Similarity NPC474086
0.6173 Remote Similarity NPC145715
0.6168 Remote Similarity NPC175585
0.6164 Remote Similarity NPC22765
0.6163 Remote Similarity NPC110615
0.6154 Remote Similarity NPC470370
0.6154 Remote Similarity NPC474528
0.6154 Remote Similarity NPC241879
0.6154 Remote Similarity NPC470369
0.6154 Remote Similarity NPC475696
0.6154 Remote Similarity NPC474415
0.6145 Remote Similarity NPC474456
0.6132 Remote Similarity NPC25340
0.6125 Remote Similarity NPC311809
0.6118 Remote Similarity NPC472831
0.6104 Remote Similarity NPC123194
0.6104 Remote Similarity NPC469770
0.6098 Remote Similarity NPC473959
0.6098 Remote Similarity NPC476559
0.6078 Remote Similarity NPC91604
0.6076 Remote Similarity NPC469769
0.6076 Remote Similarity NPC231129
0.6071 Remote Similarity NPC476135
0.6064 Remote Similarity NPC116881
0.6064 Remote Similarity NPC57163
0.6053 Remote Similarity NPC127944
0.6044 Remote Similarity NPC57599
0.6042 Remote Similarity NPC21035
0.6038 Remote Similarity NPC86906
0.6019 Remote Similarity NPC239768
0.6019 Remote Similarity NPC128698
0.6019 Remote Similarity NPC253645
0.6019 Remote Similarity NPC95920
0.6019 Remote Similarity NPC85001
0.6019 Remote Similarity NPC147835
0.6 Remote Similarity NPC98765
0.6 Remote Similarity NPC475716
0.6 Remote Similarity NPC90538
0.6 Remote Similarity NPC152211
0.6 Remote Similarity NPC28755
0.6 Remote Similarity NPC124358
0.6 Remote Similarity NPC82919
0.5982 Remote Similarity NPC246904
0.598 Remote Similarity NPC184033
0.5963 Remote Similarity NPC72753
0.5946 Remote Similarity NPC17518
0.5943 Remote Similarity NPC469958
0.5918 Remote Similarity NPC249312
0.5909 Remote Similarity NPC66862
0.5905 Remote Similarity NPC476755
0.5862 Remote Similarity NPC472543
0.5856 Remote Similarity NPC56796
0.5854 Remote Similarity NPC126458
0.5849 Remote Similarity NPC474583
0.5844 Remote Similarity NPC474416
0.5844 Remote Similarity NPC472828
0.5826 Remote Similarity NPC35037
0.5812 Remote Similarity NPC472458
0.5811 Remote Similarity NPC124851
0.581 Remote Similarity NPC34193
0.581 Remote Similarity NPC474001
0.5794 Remote Similarity NPC476921
0.5789 Remote Similarity NPC473573
0.5784 Remote Similarity NPC476261
0.5784 Remote Similarity NPC470382
0.5784 Remote Similarity NPC119225
0.5784 Remote Similarity NPC471635
0.5784 Remote Similarity NPC25033
0.5758 Remote Similarity NPC323156
0.5728 Remote Similarity NPC289140
0.5726 Remote Similarity NPC242692
0.5714 Remote Similarity NPC60408
0.5714 Remote Similarity NPC476682
0.5702 Remote Similarity NPC28280
0.5702 Remote Similarity NPC304646
0.5698 Remote Similarity NPC176107
0.5688 Remote Similarity NPC46981
0.5686 Remote Similarity NPC280710
0.5686 Remote Similarity NPC243985
0.5682 Remote Similarity NPC214770
0.5682 Remote Similarity NPC477856
0.5678 Remote Similarity NPC478138
0.566 Remote Similarity NPC476922
0.5648 Remote Similarity NPC212874
0.5636 Remote Similarity NPC476918
0.5636 Remote Similarity NPC24596
0.5632 Remote Similarity NPC20610
0.5625 Remote Similarity NPC161344

  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 NPC211322 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
0.8052 Intermediate Similarity NPD5365 Phase 2
0.6235 Remote Similarity NPD6939 Phase 2
0.6235 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6162 Remote Similarity NPD3982 Approved
0.6162 Remote Similarity NPD3980 Approved
0.6122 Remote Similarity NPD4543 Discontinued
0.6 Remote Similarity NPD7335 Phase 2
0.6 Remote Similarity NPD7337 Clinical (unspecified phase)
0.6 Remote Similarity NPD7336 Phase 2
0.6 Remote Similarity NPD2878 Approved
0.6 Remote Similarity NPD5771 Approved
0.5921 Remote Similarity NPD3722 Approved
0.5921 Remote Similarity NPD3721 Approved
0.589 Remote Similarity NPD872 Approved
0.589 Remote Similarity NPD874 Approved
0.5859 Remote Similarity NPD5915 Approved
0.5842 Remote Similarity NPD5769 Clinical (unspecified phase)
0.5784 Remote Similarity NPD5554 Approved
0.5728 Remote Similarity NPD1738 Approved
0.5714 Remote Similarity NPD4146 Approved
0.5714 Remote Similarity NPD4145 Approved
0.57 Remote Similarity NPD3346 Approved
0.57 Remote Similarity NPD3344 Approved
0.5625 Remote Similarity NPD626 Phase 3
0.5625 Remote Similarity NPD625 Approved
0.5625 Remote Similarity NPD628 Phase 3
0.5625 Remote Similarity NPD627 Approved
0.5616 Remote Similarity NPD9674 Approved
0.5616 Remote Similarity NPD9675 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