Structure

Physi-Chem Properties

Molecular Weight:  577.29
Volume:  556.094
LogP:  -0.87
LogD:  1.016
LogS:  -0.791
# Rotatable Bonds:  9
TPSA:  204.85
# H-Bond Aceptor:  11
# H-Bond Donor:  8
# Rings:  4
# Heavy Atoms:  12

MedChem Properties

QED Drug-Likeness Score:  0.179
Synthetic Accessibility Score:  5.301
Fsp3:  0.963
Lipinski Rule-of-5:  Rejected
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:  -6.18
MDCK Permeability:  9.526739449938759e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.031
Human Intestinal Absorption (HIA):  0.964
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.05
Plasma Protein Binding (PPB):  71.44054412841797%
Volume Distribution (VD):  0.421
Pgp-substrate:  13.47971248626709%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.093
CYP2C19-inhibitor:  0.006
CYP2C19-substrate:  0.491
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.214
CYP2D6-inhibitor:  0.0
CYP2D6-substrate:  0.054
CYP3A4-inhibitor:  0.018
CYP3A4-substrate:  0.032

ADMET: Excretion

Clearance (CL):  1.401
Half-life (T1/2):  0.517

ADMET: Toxicity

hERG Blockers:  0.181
Human Hepatotoxicity (H-HT):  0.35
Drug-inuced Liver Injury (DILI):  0.03
AMES Toxicity:  0.025
Rat Oral Acute Toxicity:  0.005
Maximum Recommended Daily Dose:  0.051
Skin Sensitization:  0.648
Carcinogencity:  0.013
Eye Corrosion:  0.003
Eye Irritation:  0.02
Respiratory Toxicity:  0.668

Download Data

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

  Natural Product: NPC478053

Natural Product ID:  NPC478053
Common Name*:   3beta,5,6beta,15alpha,16beta-Pentahydroxy-24-[[2-sulfo-1-(hydroxymethyl)ethyl]amino]-5alpha-cholan-24-one
IUPAC Name:   3-hydroxy-2-[[(4R)-4-[(3S,5R,6R,8R,9S,10R,13R,14S,15R,16R,17R)-3,5,6,15,16-pentahydroxy-10,13-dimethyl-1,2,3,4,6,7,8,9,11,12,14,15,16,17-tetradecahydrocyclopenta[a]phenanthren-17-yl]pentanoyl]amino]propane-1-sulfonic acid
Synonyms:  
Standard InCHIKey:  LMBOUEKKMYHDKC-LVKKNMMVSA-N
Standard InCHI:  InChI=1S/C27H47NO10S/c1-14(4-5-20(32)28-15(12-29)13-39(36,37)38)21-23(33)24(34)22-17-10-19(31)27(35)11-16(30)6-9-26(27,3)18(17)7-8-25(21,22)2/h14-19,21-24,29-31,33-35H,4-13H2,1-3H3,(H,28,32)(H,36,37,38)/t14-,15?,16+,17-,18+,19-,21+,22-,23-,24-,25-,26-,27+/m1/s1
SMILES:  C[C@H](CCC(=O)NC(CO)CS(=O)(=O)O)[C@H]1[C@H]([C@@H]([C@@H]2[C@@]1(CC[C@H]3[C@H]2C[C@H]([C@@]4([C@@]3(CC[C@@H](C4)O)C)O)O)C)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   76311392
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001445] Bile acids, alcohols and derivatives
          • [CHEMONTID:0001159] Taurinated bile acids 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
NPO26245 Styracaster caroli Species Porcellanasteridae Eukaryota n.a. n.a. n.a. PMID[8145229]
NPO26245 Styracaster caroli Species Porcellanasteridae 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
NPT24 Organism Human immunodeficiency virus 1 Human immunodeficiency virus 1 IC50 > 174000 nM PMID[8145229]
NPT3795 Organism Human immunodeficiency virus 2 Human immunodeficiency virus 2 IC50 > 174000 nM PMID[8145229]

☑ 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 NPC478053 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
0.8571 High Similarity NPC159390
0.8571 High Similarity NPC133995
0.8571 High Similarity NPC247891
0.8367 Intermediate Similarity NPC283751
0.8265 Intermediate Similarity NPC320478
0.8182 Intermediate Similarity NPC317363
0.7677 Intermediate Similarity NPC478054
0.7561 Intermediate Similarity NPC473549
0.7347 Intermediate Similarity NPC18857
0.7347 Intermediate Similarity NPC67657
0.7245 Intermediate Similarity NPC128951
0.7245 Intermediate Similarity NPC302578
0.7245 Intermediate Similarity NPC185915
0.7245 Intermediate Similarity NPC477227
0.7245 Intermediate Similarity NPC105208
0.7245 Intermediate Similarity NPC192046
0.7143 Intermediate Similarity NPC163597
0.7115 Intermediate Similarity NPC323958
0.7115 Intermediate Similarity NPC321340
0.7115 Intermediate Similarity NPC171698
0.7115 Intermediate Similarity NPC119633
0.7115 Intermediate Similarity NPC270957
0.71 Intermediate Similarity NPC287452
0.7041 Intermediate Similarity NPC158208
0.7041 Intermediate Similarity NPC243027
0.7041 Intermediate Similarity NPC317242
0.7041 Intermediate Similarity NPC196136
0.697 Remote Similarity NPC477601
0.697 Remote Similarity NPC477602
0.697 Remote Similarity NPC473916
0.6939 Remote Similarity NPC304499
0.6939 Remote Similarity NPC10476
0.6939 Remote Similarity NPC192501
0.6939 Remote Similarity NPC48795
0.6939 Remote Similarity NPC228994
0.6923 Remote Similarity NPC175419
0.6923 Remote Similarity NPC320824
0.6847 Remote Similarity NPC473287
0.6837 Remote Similarity NPC153719
0.6837 Remote Similarity NPC470610
0.6832 Remote Similarity NPC147993
0.6827 Remote Similarity NPC323180
0.6796 Remote Similarity NPC109533
0.6765 Remote Similarity NPC269333
0.6757 Remote Similarity NPC469710
0.6729 Remote Similarity NPC477600
0.6698 Remote Similarity NPC266651
0.6667 Remote Similarity NPC475325
0.6667 Remote Similarity NPC473503
0.6637 Remote Similarity NPC477226
0.6636 Remote Similarity NPC121981
0.6635 Remote Similarity NPC192456
0.6633 Remote Similarity NPC232925
0.6633 Remote Similarity NPC63588
0.6633 Remote Similarity NPC251201
0.6602 Remote Similarity NPC81074
0.6602 Remote Similarity NPC477282
0.6579 Remote Similarity NPC473638
0.6577 Remote Similarity NPC476669
0.6577 Remote Similarity NPC277774
0.6571 Remote Similarity NPC154043
0.6571 Remote Similarity NPC475388
0.6571 Remote Similarity NPC60018
0.6571 Remote Similarity NPC202688
0.6566 Remote Similarity NPC323900
0.6566 Remote Similarity NPC324984
0.6566 Remote Similarity NPC473552
0.6566 Remote Similarity NPC477821
0.6566 Remote Similarity NPC477822
0.6566 Remote Similarity NPC477823
0.6566 Remote Similarity NPC478103
0.6538 Remote Similarity NPC16449
0.6531 Remote Similarity NPC470833
0.6531 Remote Similarity NPC66407
0.6531 Remote Similarity NPC107919
0.6531 Remote Similarity NPC477820
0.6509 Remote Similarity NPC211135
0.6509 Remote Similarity NPC85095
0.6509 Remote Similarity NPC216420
0.6486 Remote Similarity NPC36372
0.6486 Remote Similarity NPC476668
0.6486 Remote Similarity NPC473637
0.6486 Remote Similarity NPC293609
0.6466 Remote Similarity NPC475518
0.6466 Remote Similarity NPC477225
0.646 Remote Similarity NPC92196
0.6455 Remote Similarity NPC109744
0.6449 Remote Similarity NPC255882
0.6436 Remote Similarity NPC478130
0.6436 Remote Similarity NPC475458
0.6435 Remote Similarity NPC473616
0.6429 Remote Similarity NPC474756
0.6408 Remote Similarity NPC64081
0.6408 Remote Similarity NPC476233
0.6408 Remote Similarity NPC133596
0.6408 Remote Similarity NPC11907
0.6408 Remote Similarity NPC474574
0.64 Remote Similarity NPC187471
0.64 Remote Similarity NPC1340
0.64 Remote Similarity NPC252182
0.64 Remote Similarity NPC470071
0.64 Remote Similarity NPC127094
0.6396 Remote Similarity NPC279329
0.6396 Remote Similarity NPC475751
0.6396 Remote Similarity NPC223143
0.6396 Remote Similarity NPC473956
0.6379 Remote Similarity NPC201712
0.6378 Remote Similarity NPC208118
0.6378 Remote Similarity NPC96080
0.6378 Remote Similarity NPC99905
0.6372 Remote Similarity NPC477224
0.6372 Remote Similarity NPC113500
0.6372 Remote Similarity NPC309866
0.6372 Remote Similarity NPC3538
0.6364 Remote Similarity NPC128475
0.6355 Remote Similarity NPC232023
0.6349 Remote Similarity NPC475887
0.6339 Remote Similarity NPC473066
0.633 Remote Similarity NPC471240
0.6327 Remote Similarity NPC63190
0.6311 Remote Similarity NPC470145
0.6306 Remote Similarity NPC20822
0.6306 Remote Similarity NPC102725
0.6306 Remote Similarity NPC473472
0.63 Remote Similarity NPC231945
0.63 Remote Similarity NPC192192
0.6293 Remote Similarity NPC475249
0.6283 Remote Similarity NPC311246
0.6283 Remote Similarity NPC167644
0.6273 Remote Similarity NPC210658
0.6273 Remote Similarity NPC5943
0.6273 Remote Similarity NPC263802
0.6273 Remote Similarity NPC474657
0.6273 Remote Similarity NPC186145
0.6273 Remote Similarity NPC161928
0.6262 Remote Similarity NPC477599
0.6239 Remote Similarity NPC273290
0.6239 Remote Similarity NPC232044
0.6224 Remote Similarity NPC44122
0.6216 Remote Similarity NPC475664
0.6216 Remote Similarity NPC281004
0.6214 Remote Similarity NPC131584
0.6214 Remote Similarity NPC139765
0.6214 Remote Similarity NPC231680
0.6214 Remote Similarity NPC91387
0.6214 Remote Similarity NPC270306
0.6207 Remote Similarity NPC473537
0.6207 Remote Similarity NPC477223
0.6207 Remote Similarity NPC316604
0.6207 Remote Similarity NPC477222
0.62 Remote Similarity NPC470830
0.62 Remote Similarity NPC129829
0.62 Remote Similarity NPC254037
0.62 Remote Similarity NPC241085
0.62 Remote Similarity NPC299948
0.6198 Remote Similarity NPC48127
0.6198 Remote Similarity NPC267217
0.6198 Remote Similarity NPC83047
0.6198 Remote Similarity NPC8009
0.6195 Remote Similarity NPC473830
0.6195 Remote Similarity NPC204881
0.6195 Remote Similarity NPC149966
0.6195 Remote Similarity NPC5632
0.619 Remote Similarity NPC471769
0.619 Remote Similarity NPC471045
0.6182 Remote Similarity NPC131365
0.6182 Remote Similarity NPC472272
0.6182 Remote Similarity NPC476727
0.6182 Remote Similarity NPC6605
0.6182 Remote Similarity NPC477283
0.6182 Remote Similarity NPC215968
0.6182 Remote Similarity NPC476726
0.6182 Remote Similarity NPC155531
0.6182 Remote Similarity NPC201273
0.6179 Remote Similarity NPC139778
0.6174 Remote Similarity NPC473065
0.6174 Remote Similarity NPC473067
0.6174 Remote Similarity NPC473064
0.6165 Remote Similarity NPC476497
0.6162 Remote Similarity NPC475172
0.6161 Remote Similarity NPC228059
0.6154 Remote Similarity NPC252564
0.6147 Remote Similarity NPC227260
0.614 Remote Similarity NPC211845
0.614 Remote Similarity NPC182740
0.614 Remote Similarity NPC256104
0.614 Remote Similarity NPC122083
0.6132 Remote Similarity NPC476176
0.6126 Remote Similarity NPC472396
0.6126 Remote Similarity NPC43912
0.6126 Remote Similarity NPC140446
0.6122 Remote Similarity NPC475943
0.6122 Remote Similarity NPC190827
0.6122 Remote Similarity NPC243469
0.6122 Remote Similarity NPC472946
0.6111 Remote Similarity NPC121121
0.6111 Remote Similarity NPC470611
0.6106 Remote Similarity NPC65550
0.6106 Remote Similarity NPC473542
0.61 Remote Similarity NPC472741

  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 NPC478053 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
0.8571 High Similarity NPD6700 Approved
0.8571 High Similarity NPD6701 Clinical (unspecified phase)
0.83 Intermediate Similarity NPD6702 Approved
0.83 Intermediate Similarity NPD6703 Approved
0.6531 Remote Similarity NPD4267 Clinical (unspecified phase)
0.6522 Remote Similarity NPD8418 Phase 2
0.6417 Remote Similarity NPD8174 Phase 2
0.6207 Remote Similarity NPD7920 Phase 3
0.6207 Remote Similarity NPD7919 Phase 3
0.6154 Remote Similarity NPD8088 Phase 1
0.6034 Remote Similarity NPD7991 Discontinued
0.6032 Remote Similarity NPD8298 Phase 2
0.598 Remote Similarity NPD4787 Phase 1
0.5941 Remote Similarity NPD6705 Phase 1
0.5888 Remote Similarity NPD5364 Discontinued
0.5862 Remote Similarity NPD8171 Discontinued
0.5782 Remote Similarity NPD7625 Phase 1
0.578 Remote Similarity NPD6928 Phase 2
0.5769 Remote Similarity NPD3187 Discontinued
0.5741 Remote Similarity NPD6697 Approved
0.5741 Remote Similarity NPD6115 Approved
0.5741 Remote Similarity NPD6118 Approved
0.5741 Remote Similarity NPD6114 Approved
0.5648 Remote Similarity NPD6116 Phase 1
0.5636 Remote Similarity NPD7525 Registered

  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