Structure

Physi-Chem Properties

Molecular Weight:  400.35
Volume:  449.537
LogP:  4.598
LogD:  3.657
LogS:  -3.612
# Rotatable Bonds:  4
TPSA:  23.55
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.595
Synthetic Accessibility Score:  4.499
Fsp3:  0.885
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:  -4.691
MDCK Permeability:  9.821007552091032e-06
Pgp-inhibitor:  0.998
Pgp-substrate:  0.742
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.043
30% Bioavailability (F30%):  0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.446
Plasma Protein Binding (PPB):  75.1703872680664%
Volume Distribution (VD):  1.09
Pgp-substrate:  20.67098617553711%

ADMET: Metabolism

CYP1A2-inhibitor:  0.043
CYP1A2-substrate:  0.226
CYP2C19-inhibitor:  0.065
CYP2C19-substrate:  0.97
CYP2C9-inhibitor:  0.038
CYP2C9-substrate:  0.07
CYP2D6-inhibitor:  0.845
CYP2D6-substrate:  0.89
CYP3A4-inhibitor:  0.828
CYP3A4-substrate:  0.906

ADMET: Excretion

Clearance (CL):  7.73
Half-life (T1/2):  0.078

ADMET: Toxicity

hERG Blockers:  0.233
Human Hepatotoxicity (H-HT):  0.449
Drug-inuced Liver Injury (DILI):  0.731
AMES Toxicity:  0.028
Rat Oral Acute Toxicity:  0.921
Maximum Recommended Daily Dose:  0.713
Skin Sensitization:  0.941
Carcinogencity:  0.66
Eye Corrosion:  0.176
Eye Irritation:  0.043
Respiratory Toxicity:  0.983

Download Data

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

  Natural Product: NPC215474

Natural Product ID:  NPC215474
Common Name*:   N-[(1S)-1-[(3S,8S,9S,10R,13S,14S,17S)-3-(Dimethylamino)-10,13-Dimethyl-2,3,4,7,8,9,11,12,14,15,16,17-Dodecahydro-1H-Cyclopenta[A]Phenanthren-17-Yl]Ethyl]-N-Methylacetamide
IUPAC Name:   N-[(1S)-1-[(3S,8S,9S,10R,13S,14S,17S)-3-(dimethylamino)-10,13-dimethyl-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-17-yl]ethyl]-N-methylacetamide
Synonyms:  
Standard InCHIKey:  DNVZSDMHLPWULM-YPWXQOIPSA-N
Standard InCHI:  InChI=1S/C26H44N2O/c1-17(28(7)18(2)29)22-10-11-23-21-9-8-19-16-20(27(5)6)12-14-25(19,3)24(21)13-15-26(22,23)4/h8,17,20-24H,9-16H2,1-7H3/p+1/t17-,20-,21-,22+,23-,24-,25-,26+/m0/s1
SMILES:  C[C@@H]([C@H]1CC[C@H]2[C@@H]3CC=C4C[C@H](CC[C@]4(C)[C@H]3CC[C@]12C)[NH+](C)C)N(C)C(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL136765
PubChem CID:   44357881
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 = 19952.62 nM PMID[525587]

☑ 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 NPC215474 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
0.9136 High Similarity NPC147513
0.9024 High Similarity NPC157479
0.8684 High Similarity NPC21773
0.8642 High Similarity NPC90150
0.8481 Intermediate Similarity NPC7214
0.8462 Intermediate Similarity NPC476904
0.8256 Intermediate Similarity NPC43308
0.8205 Intermediate Similarity NPC265789
0.8077 Intermediate Similarity NPC473442
0.8077 Intermediate Similarity NPC120167
0.7976 Intermediate Similarity NPC152039
0.7976 Intermediate Similarity NPC118329
0.7857 Intermediate Similarity NPC12035
0.7791 Intermediate Similarity NPC171639
0.7765 Intermediate Similarity NPC329782
0.7683 Intermediate Similarity NPC125828
0.7674 Intermediate Similarity NPC472312
0.7614 Intermediate Similarity NPC75810
0.7614 Intermediate Similarity NPC152684
0.7614 Intermediate Similarity NPC182106
0.7614 Intermediate Similarity NPC311769
0.7609 Intermediate Similarity NPC93027
0.7604 Intermediate Similarity NPC474001
0.759 Intermediate Similarity NPC25110
0.7586 Intermediate Similarity NPC21667
0.7558 Intermediate Similarity NPC474122
0.7529 Intermediate Similarity NPC211322
0.7528 Intermediate Similarity NPC166458
0.7396 Intermediate Similarity NPC140685
0.7363 Intermediate Similarity NPC259252
0.7347 Intermediate Similarity NPC58200
0.7222 Intermediate Similarity NPC24733
0.7188 Intermediate Similarity NPC476903
0.7172 Intermediate Similarity NPC152718
0.7159 Intermediate Similarity NPC257962
0.7129 Intermediate Similarity NPC86906
0.7079 Intermediate Similarity NPC283277
0.7019 Intermediate Similarity NPC63511
0.7009 Intermediate Similarity NPC246904
0.7 Intermediate Similarity NPC226509
0.6979 Remote Similarity NPC476754
0.6944 Remote Similarity NPC473573
0.6939 Remote Similarity NPC184033
0.6915 Remote Similarity NPC249312
0.6875 Remote Similarity NPC476752
0.6875 Remote Similarity NPC476753
0.6869 Remote Similarity NPC91604
0.6867 Remote Similarity NPC138409
0.6863 Remote Similarity NPC476921
0.6863 Remote Similarity NPC469958
0.6848 Remote Similarity NPC34811
0.6842 Remote Similarity NPC84171
0.6832 Remote Similarity NPC471083
0.6829 Remote Similarity NPC176107
0.6796 Remote Similarity NPC230677
0.6795 Remote Similarity NPC21781
0.6792 Remote Similarity NPC79238
0.6768 Remote Similarity NPC474164
0.6747 Remote Similarity NPC20610
0.6739 Remote Similarity NPC116881
0.6739 Remote Similarity NPC57163
0.6735 Remote Similarity NPC311164
0.6735 Remote Similarity NPC272732
0.6733 Remote Similarity NPC476922
0.6707 Remote Similarity NPC92327
0.6698 Remote Similarity NPC472313
0.6667 Remote Similarity NPC245223
0.6667 Remote Similarity NPC159367
0.6667 Remote Similarity NPC182815
0.6667 Remote Similarity NPC50815
0.6667 Remote Similarity NPC476918
0.6636 Remote Similarity NPC474459
0.6635 Remote Similarity NPC195841
0.6635 Remote Similarity NPC476328
0.6635 Remote Similarity NPC233256
0.6634 Remote Similarity NPC135799
0.6634 Remote Similarity NPC477964
0.6634 Remote Similarity NPC275686
0.6625 Remote Similarity NPC219621
0.6602 Remote Similarity NPC241879
0.66 Remote Similarity NPC167419
0.66 Remote Similarity NPC140300
0.6591 Remote Similarity NPC476308
0.6588 Remote Similarity NPC35734
0.6588 Remote Similarity NPC159577
0.6588 Remote Similarity NPC282593
0.6577 Remote Similarity NPC474006
0.6574 Remote Similarity NPC474452
0.6571 Remote Similarity NPC25340
0.6517 Remote Similarity NPC308050
0.6512 Remote Similarity NPC115023
0.6512 Remote Similarity NPC470078
0.6509 Remote Similarity NPC476276
0.6505 Remote Similarity NPC247060
0.6505 Remote Similarity NPC176012
0.65 Remote Similarity NPC289140
0.6476 Remote Similarity NPC476926
0.6471 Remote Similarity NPC124384
0.6463 Remote Similarity NPC53276
0.6456 Remote Similarity NPC472830
0.6442 Remote Similarity NPC90538
0.6437 Remote Similarity NPC474228
0.6437 Remote Similarity NPC303613
0.6437 Remote Similarity NPC251705
0.6415 Remote Similarity NPC46981
0.6408 Remote Similarity NPC474582
0.6408 Remote Similarity NPC118275
0.6408 Remote Similarity NPC77703
0.6404 Remote Similarity NPC259989
0.6404 Remote Similarity NPC174803
0.6395 Remote Similarity NPC214770
0.6395 Remote Similarity NPC307176
0.6395 Remote Similarity NPC477856
0.6386 Remote Similarity NPC469970
0.6381 Remote Similarity NPC212874
0.6381 Remote Similarity NPC475239
0.6381 Remote Similarity NPC119329
0.6381 Remote Similarity NPC470596
0.6374 Remote Similarity NPC120699
0.6374 Remote Similarity NPC127430
0.6356 Remote Similarity NPC79698
0.6355 Remote Similarity NPC476920
0.6355 Remote Similarity NPC476919
0.6337 Remote Similarity NPC247220
0.6322 Remote Similarity NPC234707
0.6322 Remote Similarity NPC476329
0.6321 Remote Similarity NPC55462
0.6311 Remote Similarity NPC239768
0.6311 Remote Similarity NPC128698
0.631 Remote Similarity NPC323005
0.631 Remote Similarity NPC176171
0.631 Remote Similarity NPC37792
0.63 Remote Similarity NPC280710
0.63 Remote Similarity NPC243985
0.6296 Remote Similarity NPC175585
0.6296 Remote Similarity NPC317778
0.6292 Remote Similarity NPC293803
0.6286 Remote Similarity NPC98765
0.6286 Remote Similarity NPC474583
0.6282 Remote Similarity NPC123194
0.6279 Remote Similarity NPC139397
0.6279 Remote Similarity NPC184919
0.6273 Remote Similarity NPC469968
0.6273 Remote Similarity NPC56796
0.6273 Remote Similarity NPC80834
0.625 Remote Similarity NPC470044
0.625 Remote Similarity NPC470045
0.625 Remote Similarity NPC469769
0.6222 Remote Similarity NPC474463
0.6222 Remote Similarity NPC69408
0.6216 Remote Similarity NPC478137
0.6207 Remote Similarity NPC251929
0.6207 Remote Similarity NPC40574
0.6207 Remote Similarity NPC260040
0.6207 Remote Similarity NPC265782
0.6207 Remote Similarity NPC2634
0.6207 Remote Similarity NPC475728
0.6204 Remote Similarity NPC470595
0.619 Remote Similarity NPC476755
0.618 Remote Similarity NPC309852
0.618 Remote Similarity NPC255021
0.6173 Remote Similarity NPC472827
0.6168 Remote Similarity NPC474695
0.6163 Remote Similarity NPC271640
0.6145 Remote Similarity NPC472544
0.6145 Remote Similarity NPC474086
0.6136 Remote Similarity NPC54123
0.6136 Remote Similarity NPC305501
0.6125 Remote Similarity NPC474415
0.6125 Remote Similarity NPC475696
0.6125 Remote Similarity NPC474528
0.6117 Remote Similarity NPC240650
0.6117 Remote Similarity NPC292819
0.6098 Remote Similarity NPC311809
0.6098 Remote Similarity NPC126458
0.6092 Remote Similarity NPC472831
0.6091 Remote Similarity NPC472359
0.6087 Remote Similarity NPC82635
0.6087 Remote Similarity NPC470052
0.6087 Remote Similarity NPC105197
0.6082 Remote Similarity NPC56107
0.6071 Remote Similarity NPC469662
0.6049 Remote Similarity NPC324944
0.6049 Remote Similarity NPC231129
0.6048 Remote Similarity NPC473962
0.6042 Remote Similarity NPC143344
0.6042 Remote Similarity NPC234822
0.6042 Remote Similarity NPC135639
0.6042 Remote Similarity NPC207048
0.6042 Remote Similarity NPC78058
0.6042 Remote Similarity NPC61321
0.6036 Remote Similarity NPC143173
0.6024 Remote Similarity NPC477459
0.6024 Remote Similarity NPC477461
0.6023 Remote Similarity NPC472543
0.6022 Remote Similarity NPC268580
0.6022 Remote Similarity NPC153987
0.6022 Remote Similarity NPC190211
0.6022 Remote Similarity NPC44083
0.6019 Remote Similarity NPC36497

  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 NPC215474 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
0.7126 Intermediate Similarity NPD7155 Clinical (unspecified phase)
0.6635 Remote Similarity NPD7333 Discontinued
0.6588 Remote Similarity NPD6939 Phase 2
0.6588 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6512 Remote Similarity NPD5365 Phase 2
0.6495 Remote Similarity NPD6934 Discontinued
0.6465 Remote Similarity NPD5769 Clinical (unspecified phase)
0.6395 Remote Similarity NPD4747 Approved
0.6353 Remote Similarity NPD3621 Clinical (unspecified phase)
0.63 Remote Similarity NPD5771 Approved
0.6279 Remote Similarity NPD4137 Phase 3
0.6207 Remote Similarity NPD4691 Approved
0.618 Remote Similarity NPD5733 Approved
0.6176 Remote Similarity NPD5349 Clinical (unspecified phase)
0.6136 Remote Similarity NPD4243 Approved
0.6 Remote Similarity NPD4785 Approved
0.6 Remote Similarity NPD4058 Approved
0.6 Remote Similarity NPD4687 Approved
0.6 Remote Similarity NPD4784 Approved
0.5955 Remote Similarity NPD5276 Approved
0.5938 Remote Similarity NPD3527 Clinical (unspecified phase)
0.5934 Remote Similarity NPD7339 Approved
0.5934 Remote Similarity NPD6942 Approved
0.5851 Remote Similarity NPD4195 Approved
0.5761 Remote Similarity NPD5275 Approved
0.5761 Remote Similarity NPD4190 Phase 3
0.5741 Remote Similarity NPD4803 Discontinued
0.5714 Remote Similarity NPD4786 Approved
0.5702 Remote Similarity NPD7335 Phase 2
0.5702 Remote Similarity NPD7336 Phase 2
0.5702 Remote Similarity NPD7337 Clinical (unspecified phase)
0.5673 Remote Similarity NPD5707 Approved
0.567 Remote Similarity NPD4221 Approved
0.567 Remote Similarity NPD4223 Phase 3
0.5657 Remote Similarity NPD5329 Approved
0.5644 Remote Similarity NPD4722 Approved
0.5644 Remote Similarity NPD4723 Approved
0.563 Remote Similarity NPD6345 Approved
0.563 Remote Similarity NPD6343 Approved
0.5604 Remote Similarity NPD816 Approved
0.5604 Remote Similarity NPD815 Approved
0.56 Remote Similarity NPD6098 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