Structure

Physi-Chem Properties

Molecular Weight:  502.38
Volume:  542.455
LogP:  3.845
LogD:  4.308
LogS:  -3.938
# Rotatable Bonds:  7
TPSA:  78.87
# H-Bond Aceptor:  6
# H-Bond Donor:  2
# Rings:  4
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.426
Synthetic Accessibility Score:  4.95
Fsp3:  0.867
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.842
MDCK Permeability:  1.4313300198409706e-05
Pgp-inhibitor:  0.999
Pgp-substrate:  0.859
Human Intestinal Absorption (HIA):  0.013
20% Bioavailability (F20%):  0.023
30% Bioavailability (F30%):  0.33

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.125
Plasma Protein Binding (PPB):  65.16155242919922%
Volume Distribution (VD):  1.024
Pgp-substrate:  24.641700744628906%

ADMET: Metabolism

CYP1A2-inhibitor:  0.162
CYP1A2-substrate:  0.508
CYP2C19-inhibitor:  0.113
CYP2C19-substrate:  0.92
CYP2C9-inhibitor:  0.291
CYP2C9-substrate:  0.05
CYP2D6-inhibitor:  0.592
CYP2D6-substrate:  0.865
CYP3A4-inhibitor:  0.899
CYP3A4-substrate:  0.544

ADMET: Excretion

Clearance (CL):  5.566
Half-life (T1/2):  0.378

ADMET: Toxicity

hERG Blockers:  0.674
Human Hepatotoxicity (H-HT):  0.502
Drug-inuced Liver Injury (DILI):  0.601
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.896
Maximum Recommended Daily Dose:  0.035
Skin Sensitization:  0.885
Carcinogencity:  0.245
Eye Corrosion:  0.007
Eye Irritation:  0.017
Respiratory Toxicity:  0.967

Download Data

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

  Natural Product: NPC165396

Natural Product ID:  NPC165396
Common Name*:   Acetic Acid (1S,4S,6R,7R,10R,11S,12S,15S,16S)-17-((S)-1-Dimethylamino-Ethyl)-2-(S)-Hydroxy-10,13-Dimethyl-3-((E)-2-Methyl-But-2-Enoylamino)-Hexadecahydro-Cyclopenta[A]Phenanthren-4-Yl Ester
IUPAC Name:   [(2S,3S,4R,5R,8S,9S,10R,13S,14S,17S)-17-[(1S)-1-(dimethylamino)ethyl]-2-hydroxy-10,13-dimethyl-3-[[(E)-2-methylbut-2-enoyl]amino]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-4-yl] acetate
Synonyms:  
Standard InCHIKey:  QDWARQARJPJBNM-MZHFMOSXSA-N
Standard InCHI:  InChI=1S/C30H50N2O4/c1-9-17(2)28(35)31-26-25(34)16-30(6)23-14-15-29(5)21(18(3)32(7)8)12-13-22(29)20(23)10-11-24(30)27(26)36-19(4)33/h9,18,20-27,34H,10-16H2,1-8H3,(H,31,35)/b17-9+/t18-,20-,21+,22-,23-,24-,25-,26-,27+,29+,30+/m0/s1
SMILES:  C/C=C(C)/C(=N[C@H]1[C@H](C[C@]2(C)[C@H]3CC[C@]4(C)[C@H](CC[C@H]4[C@@H]3CC[C@H]2[C@H]1OC(=O)C)[C@H](C)N(C)C)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL421920
PubChem CID:   15043264
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001194] Oxosteroids
          • [CHEMONTID:0003060] 16-oxosteroids

*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
NPT2668 Individual Protein Acetylcholinesterase Torpedo californica IC50 = 182400.0 nM PMID[537132]
NPT439 Individual Protein Butyrylcholinesterase Homo sapiens IC50 = 18200.0 nM PMID[537132]
NPT204 Individual Protein Acetylcholinesterase Homo sapiens IC50 = 181970.09 nM PMID[537133]

☑ 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 NPC165396 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
0.9375 High Similarity NPC242692
0.9123 High Similarity NPC472458
0.8972 High Similarity NPC36497
0.8739 High Similarity NPC66862
0.8729 High Similarity NPC237286
0.8482 Intermediate Similarity NPC72753
0.8482 Intermediate Similarity NPC472359
0.8333 Intermediate Similarity NPC469968
0.8333 Intermediate Similarity NPC80834
0.7857 Intermediate Similarity NPC471083
0.7807 Intermediate Similarity NPC55462
0.7544 Intermediate Similarity NPC50815
0.7518 Intermediate Similarity NPC275839
0.7391 Intermediate Similarity NPC247060
0.7288 Intermediate Similarity NPC25340
0.7222 Intermediate Similarity NPC270957
0.7222 Intermediate Similarity NPC171698
0.7222 Intermediate Similarity NPC321340
0.7222 Intermediate Similarity NPC119633
0.7179 Intermediate Similarity NPC474583
0.7131 Intermediate Similarity NPC56796
0.7105 Intermediate Similarity NPC476903
0.7037 Intermediate Similarity NPC175419
0.6967 Remote Similarity NPC472313
0.6964 Remote Similarity NPC53890
0.6964 Remote Similarity NPC219937
0.6964 Remote Similarity NPC123252
0.6964 Remote Similarity NPC194485
0.6944 Remote Similarity NPC323180
0.6929 Remote Similarity NPC35037
0.6917 Remote Similarity NPC86906
0.6916 Remote Similarity NPC257962
0.6911 Remote Similarity NPC474459
0.6891 Remote Similarity NPC90538
0.6881 Remote Similarity NPC299963
0.6875 Remote Similarity NPC470593
0.6875 Remote Similarity NPC470594
0.6855 Remote Similarity NPC474452
0.6842 Remote Similarity NPC26046
0.6833 Remote Similarity NPC470596
0.6822 Remote Similarity NPC476504
0.6814 Remote Similarity NPC10274
0.681 Remote Similarity NPC276103
0.681 Remote Similarity NPC54248
0.68 Remote Similarity NPC478137
0.6786 Remote Similarity NPC160304
0.6783 Remote Similarity NPC474922
0.6777 Remote Similarity NPC258130
0.6769 Remote Similarity NPC469943
0.6754 Remote Similarity NPC219516
0.6754 Remote Similarity NPC130840
0.675 Remote Similarity NPC189588
0.675 Remote Similarity NPC241879
0.675 Remote Similarity NPC187302
0.675 Remote Similarity NPC196471
0.675 Remote Similarity NPC97487
0.675 Remote Similarity NPC10232
0.6724 Remote Similarity NPC241047
0.6697 Remote Similarity NPC472504
0.6695 Remote Similarity NPC102426
0.6695 Remote Similarity NPC119036
0.6695 Remote Similarity NPC300179
0.6695 Remote Similarity NPC275086
0.6695 Remote Similarity NPC325229
0.6694 Remote Similarity NPC119329
0.6693 Remote Similarity NPC476502
0.6667 Remote Similarity NPC306797
0.6667 Remote Similarity NPC292718
0.6667 Remote Similarity NPC111834
0.6667 Remote Similarity NPC476503
0.6667 Remote Similarity NPC217801
0.6667 Remote Similarity NPC470595
0.6667 Remote Similarity NPC152684
0.6667 Remote Similarity NPC169270
0.6642 Remote Similarity NPC476497
0.664 Remote Similarity NPC79238
0.6639 Remote Similarity NPC251680
0.6638 Remote Similarity NPC3359
0.6613 Remote Similarity NPC218602
0.6612 Remote Similarity NPC473523
0.6612 Remote Similarity NPC222153
0.6612 Remote Similarity NPC45365
0.6612 Remote Similarity NPC293299
0.661 Remote Similarity NPC51499
0.661 Remote Similarity NPC292819
0.661 Remote Similarity NPC4834
0.6609 Remote Similarity NPC234335
0.6607 Remote Similarity NPC323958
0.6607 Remote Similarity NPC168231
0.6606 Remote Similarity NPC109533
0.6589 Remote Similarity NPC471118
0.6589 Remote Similarity NPC471121
0.6585 Remote Similarity NPC267217
0.6585 Remote Similarity NPC48127
0.6585 Remote Similarity NPC8009
0.6585 Remote Similarity NPC83047
0.6583 Remote Similarity NPC222875
0.6583 Remote Similarity NPC295110
0.6583 Remote Similarity NPC25177
0.6583 Remote Similarity NPC268829
0.6583 Remote Similarity NPC475617
0.6583 Remote Similarity NPC289670
0.6583 Remote Similarity NPC247701
0.6579 Remote Similarity NPC235460
0.6567 Remote Similarity NPC476501
0.6562 Remote Similarity NPC203005
0.6557 Remote Similarity NPC473543
0.6535 Remote Similarity NPC106479
0.6532 Remote Similarity NPC472218
0.6532 Remote Similarity NPC472219
0.6532 Remote Similarity NPC472217
0.6532 Remote Similarity NPC159367
0.6529 Remote Similarity NPC476471
0.6529 Remote Similarity NPC475344
0.6525 Remote Similarity NPC304899
0.6525 Remote Similarity NPC471903
0.6525 Remote Similarity NPC253115
0.6518 Remote Similarity NPC164424
0.6512 Remote Similarity NPC471120
0.6512 Remote Similarity NPC471117
0.6504 Remote Similarity NPC119855
0.6504 Remote Similarity NPC220217
0.65 Remote Similarity NPC180733
0.65 Remote Similarity NPC132847
0.65 Remote Similarity NPC37047
0.65 Remote Similarity NPC275686
0.65 Remote Similarity NPC41971
0.6496 Remote Similarity NPC475472
0.6496 Remote Similarity NPC90814
0.6496 Remote Similarity NPC189393
0.6484 Remote Similarity NPC470540
0.648 Remote Similarity NPC475030
0.6475 Remote Similarity NPC160583
0.6475 Remote Similarity NPC474124
0.6471 Remote Similarity NPC274793
0.6471 Remote Similarity NPC140300
0.6471 Remote Similarity NPC240650
0.6463 Remote Similarity NPC298005
0.6463 Remote Similarity NPC36463
0.6462 Remote Similarity NPC9714
0.646 Remote Similarity NPC474970
0.6457 Remote Similarity NPC477291
0.6452 Remote Similarity NPC475781
0.6452 Remote Similarity NPC169375
0.6449 Remote Similarity NPC73829
0.6449 Remote Similarity NPC119794
0.6446 Remote Similarity NPC96784
0.6446 Remote Similarity NPC121218
0.6446 Remote Similarity NPC253886
0.6446 Remote Similarity NPC75941
0.6446 Remote Similarity NPC235920
0.6441 Remote Similarity NPC279974
0.6429 Remote Similarity NPC139778
0.6429 Remote Similarity NPC102048
0.6417 Remote Similarity NPC218107
0.641 Remote Similarity NPC476304
0.641 Remote Similarity NPC38232
0.6403 Remote Similarity NPC76999
0.6396 Remote Similarity NPC202688
0.6396 Remote Similarity NPC154043
0.6396 Remote Similarity NPC60018
0.6393 Remote Similarity NPC476755
0.6393 Remote Similarity NPC152718
0.6391 Remote Similarity NPC478138
0.6387 Remote Similarity NPC88009
0.6387 Remote Similarity NPC195366
0.6387 Remote Similarity NPC289140
0.6387 Remote Similarity NPC114743
0.6372 Remote Similarity NPC266651
0.6372 Remote Similarity NPC75810
0.6371 Remote Similarity NPC186668
0.637 Remote Similarity NPC473922
0.6364 Remote Similarity NPC94906
0.6364 Remote Similarity NPC208358
0.6364 Remote Similarity NPC206735
0.6364 Remote Similarity NPC201712
0.6357 Remote Similarity NPC280941
0.6357 Remote Similarity NPC75318
0.6357 Remote Similarity NPC235772
0.6357 Remote Similarity NPC476499
0.6356 Remote Similarity NPC279410
0.6356 Remote Similarity NPC144202
0.6356 Remote Similarity NPC119562
0.6356 Remote Similarity NPC476186
0.6356 Remote Similarity NPC280710
0.6356 Remote Similarity NPC243985
0.6349 Remote Similarity NPC257082
0.6341 Remote Similarity NPC45897
0.6341 Remote Similarity NPC472821
0.6339 Remote Similarity NPC5280
0.6339 Remote Similarity NPC473742
0.6336 Remote Similarity NPC470276
0.6333 Remote Similarity NPC476893
0.6333 Remote Similarity NPC210337
0.6333 Remote Similarity NPC475032
0.6333 Remote Similarity NPC475033
0.6333 Remote Similarity NPC253586
0.6328 Remote Similarity NPC124358
0.6325 Remote Similarity NPC110923
0.6325 Remote Similarity NPC74296

  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 NPC165396 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
0.7236 Intermediate Similarity NPD7755 Approved
0.7236 Intermediate Similarity NPD7754 Approved
0.7217 Intermediate Similarity NPD8418 Phase 2
0.7073 Intermediate Similarity NPD8298 Phase 2
0.7 Intermediate Similarity NPD7646 Clinical (unspecified phase)
0.6855 Remote Similarity NPD8078 Approved
0.6855 Remote Similarity NPD8077 Approved
0.6667 Remote Similarity NPD8174 Phase 2
0.6639 Remote Similarity NPD7640 Approved
0.6639 Remote Similarity NPD6920 Discontinued
0.6639 Remote Similarity NPD7639 Approved
0.6612 Remote Similarity NPD7986 Approved
0.6612 Remote Similarity NPD7987 Approved
0.6612 Remote Similarity NPD7912 Approved
0.6612 Remote Similarity NPD7911 Approved
0.6555 Remote Similarity NPD7638 Approved
0.6504 Remote Similarity NPD8040 Discontinued
0.6496 Remote Similarity NPD5771 Approved
0.6452 Remote Similarity NPD7989 Approved
0.6452 Remote Similarity NPD7990 Approved
0.64 Remote Similarity NPD6415 Discontinued
0.6316 Remote Similarity NPD6909 Approved
0.6316 Remote Similarity NPD6908 Approved
0.6198 Remote Similarity NPD7920 Phase 3
0.6198 Remote Similarity NPD7919 Phase 3
0.6187 Remote Similarity NPD6914 Discontinued
0.6174 Remote Similarity NPD8308 Discontinued
0.6167 Remote Similarity NPD7991 Discontinued
0.6148 Remote Similarity NPD8088 Phase 1
0.6129 Remote Similarity NPD7632 Discontinued
0.6111 Remote Similarity NPD7333 Discontinued
0.6102 Remote Similarity NPD6701 Clinical (unspecified phase)
0.6102 Remote Similarity NPD6700 Approved
0.609 Remote Similarity NPD7328 Approved
0.609 Remote Similarity NPD7327 Approved
0.605 Remote Similarity NPD7637 Suspended
0.6047 Remote Similarity NPD6421 Discontinued
0.6045 Remote Similarity NPD7516 Approved
0.6036 Remote Similarity NPD6114 Approved
0.6036 Remote Similarity NPD6115 Approved
0.6036 Remote Similarity NPD6118 Approved
0.6036 Remote Similarity NPD6697 Approved
0.6 Remote Similarity NPD6333 Approved
0.6 Remote Similarity NPD7625 Phase 1
0.6 Remote Similarity NPD6334 Approved
0.5984 Remote Similarity NPD6640 Phase 3
0.5984 Remote Similarity NPD5357 Phase 1
0.5956 Remote Similarity NPD6921 Approved
0.5956 Remote Similarity NPD8296 Approved
0.5956 Remote Similarity NPD8335 Approved
0.5956 Remote Similarity NPD8380 Approved
0.5956 Remote Similarity NPD8378 Approved
0.5956 Remote Similarity NPD8379 Approved
0.5948 Remote Similarity NPD7520 Clinical (unspecified phase)
0.5946 Remote Similarity NPD8143 Approved
0.5946 Remote Similarity NPD8144 Approved
0.5929 Remote Similarity NPD7525 Registered
0.5923 Remote Similarity NPD6420 Discontinued
0.5917 Remote Similarity NPD6702 Approved
0.5917 Remote Similarity NPD6703 Approved
0.5917 Remote Similarity NPD8034 Phase 2
0.5917 Remote Similarity NPD8035 Phase 2
0.5913 Remote Similarity NPD6695 Phase 3
0.5882 Remote Similarity NPD8294 Approved
0.5882 Remote Similarity NPD8377 Approved
0.5868 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5862 Remote Similarity NPD7338 Clinical (unspecified phase)
0.5856 Remote Similarity NPD6117 Approved
0.5855 Remote Similarity NPD7274 Clinical (unspecified phase)
0.5854 Remote Similarity NPD5349 Clinical (unspecified phase)
0.584 Remote Similarity NPD6404 Discontinued
0.5839 Remote Similarity NPD8033 Approved
0.582 Remote Similarity NPD5769 Clinical (unspecified phase)
0.5804 Remote Similarity NPD6116 Phase 1
0.5739 Remote Similarity NPD1448 Clinical (unspecified phase)
0.5738 Remote Similarity NPD6399 Phase 3
0.5736 Remote Similarity NPD6675 Approved
0.5736 Remote Similarity NPD5739 Approved
0.5736 Remote Similarity NPD7128 Approved
0.5736 Remote Similarity NPD6402 Approved
0.5714 Remote Similarity NPD7524 Approved
0.5714 Remote Similarity NPD7750 Discontinued
0.5704 Remote Similarity NPD6940 Discontinued
0.5702 Remote Similarity NPD6929 Approved
0.5695 Remote Similarity NPD2174 Clinical (unspecified phase)
0.5691 Remote Similarity NPD5707 Approved
0.5676 Remote Similarity NPD6113 Clinical (unspecified phase)
0.5674 Remote Similarity NPD7507 Approved
0.5667 Remote Similarity NPD4264 Clinical (unspecified phase)
0.5664 Remote Similarity NPD7319 Approved
0.5662 Remote Similarity NPD7115 Discovery
0.5655 Remote Similarity NPD8338 Approved
0.5655 Remote Similarity NPD8449 Approved
0.5652 Remote Similarity NPD6930 Phase 2
0.5652 Remote Similarity NPD6931 Approved
0.5649 Remote Similarity NPD6899 Approved
0.5649 Remote Similarity NPD6881 Approved
0.5649 Remote Similarity NPD7320 Approved
0.5646 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5643 Remote Similarity NPD7604 Phase 2
0.5635 Remote Similarity NPD4225 Approved
0.562 Remote Similarity NPD6051 Approved
0.5616 Remote Similarity NPD8450 Suspended
0.5612 Remote Similarity NPD7503 Approved
0.5606 Remote Similarity NPD6372 Approved
0.5606 Remote Similarity NPD6373 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