Structure

Physi-Chem Properties

Molecular Weight:  458.39
Volume:  504.295
LogP:  5.525
LogD:  4.951
LogS:  -5.08
# Rotatable Bonds:  4
TPSA:  43.78
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  5
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.6
Synthetic Accessibility Score:  4.946
Fsp3:  0.966
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.794
MDCK Permeability:  9.143450370174833e-06
Pgp-inhibitor:  0.995
Pgp-substrate:  0.342
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.814
30% Bioavailability (F30%):  0.19

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.176
Plasma Protein Binding (PPB):  82.66484069824219%
Volume Distribution (VD):  0.932
Pgp-substrate:  5.303637504577637%

ADMET: Metabolism

CYP1A2-inhibitor:  0.032
CYP1A2-substrate:  0.203
CYP2C19-inhibitor:  0.037
CYP2C19-substrate:  0.97
CYP2C9-inhibitor:  0.1
CYP2C9-substrate:  0.081
CYP2D6-inhibitor:  0.148
CYP2D6-substrate:  0.87
CYP3A4-inhibitor:  0.804
CYP3A4-substrate:  0.87

ADMET: Excretion

Clearance (CL):  13.92
Half-life (T1/2):  0.086

ADMET: Toxicity

hERG Blockers:  0.668
Human Hepatotoxicity (H-HT):  0.356
Drug-inuced Liver Injury (DILI):  0.861
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.852
Maximum Recommended Daily Dose:  0.039
Skin Sensitization:  0.942
Carcinogencity:  0.342
Eye Corrosion:  0.042
Eye Irritation:  0.017
Respiratory Toxicity:  0.96

Download Data

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

  Natural Product: NPC292819

Natural Product ID:  NPC292819
Common Name*:   Pachystermine B
IUPAC Name:   (3R)-1-[(3S,4R,5R,8S,9S,10R,13S,14S,17S)-17-[(1S)-1-(dimethylamino)ethyl]-4-hydroxy-10,13-dimethyl-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-3-yl]-3-propan-2-ylazetidin-2-one
Synonyms:   Pachystermine B
Standard InCHIKey:  AENZWKGHCPXWBZ-APKZJJHSSA-N
Standard InCHI:  InChI=1S/C29H50N2O2/c1-17(2)20-16-31(27(20)33)25-13-15-29(5)23-12-14-28(4)21(18(3)30(6)7)10-11-22(28)19(23)8-9-24(29)26(25)32/h17-26,32H,8-16H2,1-7H3/t18-,19-,20-,21+,22-,23-,24-,25-,26+,28+,29+/m0/s1
SMILES:  CC(C)[C@@H]1CN([C@H]2CC[C@]3(C)[C@H]4CC[C@]5(C)[C@H](CC[C@H]5[C@@H]4CC[C@H]3[C@H]2O)[C@H](C)N(C)C)C1=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2087206
PubChem CID:   70695310
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001295] Hydroxysteroids

*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
NPO13852 Pachysandra terminalis Species Buxaceae Eukaryota n.a. n.a. n.a. PMID[22804108]
NPO13852 Pachysandra terminalis Species Buxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13852 Pachysandra terminalis Species Buxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13852 Pachysandra terminalis Species Buxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13852 Pachysandra terminalis 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
NPT82 Cell Line MDA-MB-231 Homo sapiens IC50 = 190.0 nM PMID[538461]

☑ 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 NPC292819 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
0.9175 High Similarity NPC470596
0.89 High Similarity NPC470595
0.8586 High Similarity NPC470592
0.8182 Intermediate Similarity NPC470593
0.8182 Intermediate Similarity NPC470594
0.7604 Intermediate Similarity NPC34811
0.7576 Intermediate Similarity NPC312637
0.7553 Intermediate Similarity NPC109533
0.7404 Intermediate Similarity NPC220111
0.7222 Intermediate Similarity NPC120167
0.7222 Intermediate Similarity NPC473442
0.7115 Intermediate Similarity NPC174117
0.7069 Intermediate Similarity NPC474006
0.7048 Intermediate Similarity NPC476903
0.6981 Remote Similarity NPC473537
0.6964 Remote Similarity NPC473994
0.6931 Remote Similarity NPC21035
0.6916 Remote Similarity NPC475249
0.6916 Remote Similarity NPC252564
0.6909 Remote Similarity NPC475239
0.6887 Remote Similarity NPC289140
0.6881 Remote Similarity NPC476755
0.6852 Remote Similarity NPC201712
0.6847 Remote Similarity NPC36497
0.6842 Remote Similarity NPC25110
0.6818 Remote Similarity NPC241879
0.6789 Remote Similarity NPC475518
0.6783 Remote Similarity NPC124358
0.6696 Remote Similarity NPC55462
0.6637 Remote Similarity NPC25340
0.6635 Remote Similarity NPC135005
0.6634 Remote Similarity NPC175419
0.661 Remote Similarity NPC165396
0.6583 Remote Similarity NPC475340
0.6579 Remote Similarity NPC159367
0.6577 Remote Similarity NPC471083
0.6559 Remote Similarity NPC124384
0.6552 Remote Similarity NPC66862
0.6535 Remote Similarity NPC323180
0.6526 Remote Similarity NPC232112
0.6505 Remote Similarity NPC171698
0.6505 Remote Similarity NPC119633
0.6505 Remote Similarity NPC321340
0.6505 Remote Similarity NPC270957
0.65 Remote Similarity NPC90150
0.65 Remote Similarity NPC192456
0.6496 Remote Similarity NPC56796
0.6491 Remote Similarity NPC48127
0.6491 Remote Similarity NPC244982
0.6491 Remote Similarity NPC83047
0.6491 Remote Similarity NPC476756
0.6491 Remote Similarity NPC267217
0.6491 Remote Similarity NPC8009
0.6476 Remote Similarity NPC323156
0.6466 Remote Similarity NPC472359
0.6466 Remote Similarity NPC72753
0.6421 Remote Similarity NPC151018
0.6421 Remote Similarity NPC156277
0.6421 Remote Similarity NPC320549
0.6421 Remote Similarity NPC58057
0.6392 Remote Similarity NPC212733
0.6392 Remote Similarity NPC273366
0.6392 Remote Similarity NPC21220
0.6392 Remote Similarity NPC195155
0.6392 Remote Similarity NPC125767
0.6392 Remote Similarity NPC174964
0.6392 Remote Similarity NPC97534
0.6383 Remote Similarity NPC245223
0.6372 Remote Similarity NPC474583
0.6356 Remote Similarity NPC80834
0.6356 Remote Similarity NPC469968
0.633 Remote Similarity NPC155985
0.6327 Remote Similarity NPC472486
0.6327 Remote Similarity NPC475742
0.6327 Remote Similarity NPC4209
0.6327 Remote Similarity NPC5767
0.6327 Remote Similarity NPC472487
0.6325 Remote Similarity NPC139778
0.6303 Remote Similarity NPC28224
0.6289 Remote Similarity NPC280026
0.6289 Remote Similarity NPC254340
0.6289 Remote Similarity NPC167702
0.6271 Remote Similarity NPC474459
0.6264 Remote Similarity NPC114891
0.6263 Remote Similarity NPC475031
0.6263 Remote Similarity NPC143133
0.6263 Remote Similarity NPC221420
0.6263 Remote Similarity NPC317913
0.6263 Remote Similarity NPC23884
0.6263 Remote Similarity NPC207010
0.6263 Remote Similarity NPC298168
0.6261 Remote Similarity NPC86906
0.626 Remote Similarity NPC96080
0.626 Remote Similarity NPC99905
0.626 Remote Similarity NPC208118
0.625 Remote Similarity NPC89310
0.625 Remote Similarity NPC147513
0.6237 Remote Similarity NPC142712
0.6218 Remote Similarity NPC474452
0.6211 Remote Similarity NPC213178
0.6211 Remote Similarity NPC327728
0.6211 Remote Similarity NPC131892
0.6211 Remote Similarity NPC6120
0.621 Remote Similarity NPC242692
0.62 Remote Similarity NPC224802
0.62 Remote Similarity NPC324700
0.62 Remote Similarity NPC34046
0.62 Remote Similarity NPC171426
0.62 Remote Similarity NPC80089
0.6195 Remote Similarity NPC474001
0.619 Remote Similarity NPC323958
0.6186 Remote Similarity NPC310766
0.6186 Remote Similarity NPC472313
0.6172 Remote Similarity NPC476497
0.617 Remote Similarity NPC475884
0.617 Remote Similarity NPC48079
0.617 Remote Similarity NPC473230
0.6167 Remote Similarity NPC478137
0.6154 Remote Similarity NPC71460
0.6154 Remote Similarity NPC148174
0.6154 Remote Similarity NPC218585
0.6147 Remote Similarity NPC93027
0.614 Remote Similarity NPC50815
0.6139 Remote Similarity NPC80891
0.6139 Remote Similarity NPC320144
0.6139 Remote Similarity NPC201276
0.6132 Remote Similarity NPC43308
0.6132 Remote Similarity NPC168017
0.6129 Remote Similarity NPC473276
0.6129 Remote Similarity NPC41577
0.6129 Remote Similarity NPC474380
0.6117 Remote Similarity NPC215474
0.6111 Remote Similarity NPC21781
0.6105 Remote Similarity NPC472741
0.6098 Remote Similarity NPC475887
0.6094 Remote Similarity NPC476501
0.609 Remote Similarity NPC474210
0.6083 Remote Similarity NPC476498
0.6071 Remote Similarity NPC140300
0.6068 Remote Similarity NPC46981
0.6066 Remote Similarity NPC476502
0.6066 Remote Similarity NPC476955
0.6064 Remote Similarity NPC44122
0.6061 Remote Similarity NPC477002
0.6061 Remote Similarity NPC159789
0.605 Remote Similarity NPC63511
0.6042 Remote Similarity NPC477820
0.6042 Remote Similarity NPC299948
0.6042 Remote Similarity NPC319671
0.6042 Remote Similarity NPC469941
0.6042 Remote Similarity NPC129829
0.6042 Remote Similarity NPC241085
0.6042 Remote Similarity NPC470830
0.6042 Remote Similarity NPC321732
0.6042 Remote Similarity NPC66407
0.6042 Remote Similarity NPC254037
0.6042 Remote Similarity NPC476734
0.6042 Remote Similarity NPC324607
0.6042 Remote Similarity NPC252032
0.6042 Remote Similarity NPC107919
0.604 Remote Similarity NPC185465
0.6038 Remote Similarity NPC157479
0.6036 Remote Similarity NPC272732
0.6036 Remote Similarity NPC311164
0.6032 Remote Similarity NPC472458
0.6022 Remote Similarity NPC118937
0.6022 Remote Similarity NPC69149
0.6022 Remote Similarity NPC167995
0.6022 Remote Similarity NPC281540
0.6022 Remote Similarity NPC159654
0.6019 Remote Similarity NPC469745
0.6019 Remote Similarity NPC58631
0.6019 Remote Similarity NPC12933
0.6019 Remote Similarity NPC178632
0.6018 Remote Similarity NPC91604
0.6017 Remote Similarity NPC476276
0.6016 Remote Similarity NPC221196
0.6016 Remote Similarity NPC39485
0.6 Remote Similarity NPC476735
0.6 Remote Similarity NPC309249
0.6 Remote Similarity NPC79238
0.6 Remote Similarity NPC63190
0.6 Remote Similarity NPC247060
0.5984 Remote Similarity NPC476499
0.5979 Remote Similarity NPC192192
0.5979 Remote Similarity NPC477929
0.5979 Remote Similarity NPC63588
0.5979 Remote Similarity NPC232925
0.5979 Remote Similarity NPC282454
0.5979 Remote Similarity NPC251201
0.5979 Remote Similarity NPC231945
0.5965 Remote Similarity NPC135799
0.5962 Remote Similarity NPC289486
0.5962 Remote Similarity NPC30583
0.5962 Remote Similarity NPC61107
0.5962 Remote Similarity NPC268040
0.5962 Remote Similarity NPC121121
0.596 Remote Similarity NPC133922
0.596 Remote Similarity NPC472854
0.5948 Remote Similarity NPC98765

  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 NPC292819 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
0.7477 Intermediate Similarity NPD6920 Discontinued
0.7339 Intermediate Similarity NPD6415 Discontinued
0.7168 Intermediate Similarity NPD8298 Phase 2
0.7091 Intermediate Similarity NPD7646 Clinical (unspecified phase)
0.6981 Remote Similarity NPD7920 Phase 3
0.6981 Remote Similarity NPD7919 Phase 3
0.6916 Remote Similarity NPD8088 Phase 1
0.6852 Remote Similarity NPD8418 Phase 2
0.6847 Remote Similarity NPD8040 Discontinued
0.6667 Remote Similarity NPD7911 Approved
0.6667 Remote Similarity NPD7986 Approved
0.6667 Remote Similarity NPD7912 Approved
0.6667 Remote Similarity NPD7987 Approved
0.6633 Remote Similarity NPD7155 Clinical (unspecified phase)
0.661 Remote Similarity NPD7755 Approved
0.661 Remote Similarity NPD7754 Approved
0.6571 Remote Similarity NPD6934 Discontinued
0.6491 Remote Similarity NPD7989 Approved
0.6491 Remote Similarity NPD7990 Approved
0.6421 Remote Similarity NPD4808 Clinical (unspecified phase)
0.6421 Remote Similarity NPD4809 Clinical (unspecified phase)
0.6356 Remote Similarity NPD8078 Approved
0.6356 Remote Similarity NPD8077 Approved
0.6346 Remote Similarity NPD8308 Discontinued
0.6327 Remote Similarity NPD6117 Approved
0.6289 Remote Similarity NPD6113 Clinical (unspecified phase)
0.6263 Remote Similarity NPD6116 Phase 1
0.6211 Remote Similarity NPD3699 Clinical (unspecified phase)
0.6211 Remote Similarity NPD3700 Clinical (unspecified phase)
0.62 Remote Similarity NPD6114 Approved
0.62 Remote Similarity NPD6697 Approved
0.62 Remote Similarity NPD6115 Approved
0.62 Remote Similarity NPD6118 Approved
0.6182 Remote Similarity NPD7991 Discontinued
0.6146 Remote Similarity NPD4789 Approved
0.6146 Remote Similarity NPD4245 Approved
0.6146 Remote Similarity NPD4244 Approved
0.6121 Remote Similarity NPD7333 Discontinued
0.61 Remote Similarity NPD8143 Approved
0.61 Remote Similarity NPD8144 Approved
0.6061 Remote Similarity NPD3703 Phase 2
0.6042 Remote Similarity NPD3698 Phase 2
0.6042 Remote Similarity NPD4267 Clinical (unspecified phase)
0.6018 Remote Similarity NPD3104 Approved
0.6018 Remote Similarity NPD3102 Approved
0.6018 Remote Similarity NPD3101 Approved
0.6018 Remote Similarity NPD3103 Approved
0.5957 Remote Similarity NPD3171 Clinical (unspecified phase)
0.5943 Remote Similarity NPD3723 Clinical (unspecified phase)
0.5938 Remote Similarity NPD5361 Clinical (unspecified phase)
0.5938 Remote Similarity NPD5360 Phase 3
0.5906 Remote Similarity NPD7652 Discontinued
0.5818 Remote Similarity NPD6700 Approved
0.5818 Remote Similarity NPD6701 Clinical (unspecified phase)
0.5816 Remote Similarity NPD4787 Phase 1
0.5804 Remote Similarity NPD2636 Clinical (unspecified phase)
0.5804 Remote Similarity NPD2637 Approved
0.5794 Remote Similarity NPD7520 Clinical (unspecified phase)
0.5773 Remote Similarity NPD6705 Phase 1
0.5766 Remote Similarity NPD6702 Approved
0.5766 Remote Similarity NPD6703 Approved
0.575 Remote Similarity NPD8174 Phase 2
0.5728 Remote Similarity NPD3671 Phase 1
0.5645 Remote Similarity NPD1376 Discontinued
0.56 Remote Similarity NPD6081 Approved
0.56 Remote Similarity NPD4758 Discontinued

  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