Structure

Physi-Chem Properties

Molecular Weight:  685.24
Volume:  632.969
LogP:  4.433
LogD:  2.624
LogS:  -6.19
# Rotatable Bonds:  11
TPSA:  199.29
# H-Bond Aceptor:  12
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  15

MedChem Properties

QED Drug-Likeness Score:  0.231
Synthetic Accessibility Score:  5.821
Fsp3:  1.0
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:  -4.945
MDCK Permeability:  5.3624051361111924e-05
Pgp-inhibitor:  0.999
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.045
20% Bioavailability (F20%):  0.018
30% Bioavailability (F30%):  0.304

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.011
Plasma Protein Binding (PPB):  96.79314422607422%
Volume Distribution (VD):  1.392
Pgp-substrate:  2.8804543018341064%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.389
CYP2C19-inhibitor:  0.007
CYP2C19-substrate:  0.914
CYP2C9-inhibitor:  0.086
CYP2C9-substrate:  0.1
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.18
CYP3A4-inhibitor:  0.023
CYP3A4-substrate:  0.078

ADMET: Excretion

Clearance (CL):  2.063
Half-life (T1/2):  0.001

ADMET: Toxicity

hERG Blockers:  0.929
Human Hepatotoxicity (H-HT):  0.867
Drug-inuced Liver Injury (DILI):  0.93
AMES Toxicity:  0.714
Rat Oral Acute Toxicity:  0.976
Maximum Recommended Daily Dose:  0.961
Skin Sensitization:  0.995
Carcinogencity:  0.863
Eye Corrosion:  0.999
Eye Irritation:  0.908
Respiratory Toxicity:  0.995

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

  Natural Product: NPC473552

Natural Product ID:  NPC473552
Common Name*:   Halistanol Sulfate
IUPAC Name:   trisodium;[(2S,3S,5S,6S,8S,9S,10R,13R,14S,17R)-10,13-dimethyl-2,3-disulfonatooxy-17-[(2R)-5,6,6-trimethylheptan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-6-yl] sulfate
Synonyms:   Halistanol Sulfate
Standard InCHIKey:  SPEMVTYJKSAHEG-DGLFYPOVSA-K
Standard InCHI:  InChI=1S/C29H52O12S3.3Na/c1-17(8-9-18(2)27(3,4)5)20-10-11-21-19-14-24(39-42(30,31)32)23-15-25(40-43(33,34)35)26(41-44(36,37)38)16-29(23,7)22(19)12-13-28(20,21)6;;;/h17-26H,8-16H2,1-7H3,(H,30,31,32)(H,33,34,35)(H,36,37,38);;;/q;3*+1/p-3/t17-,18?,19+,20-,21+,22+,23-,24+,25+,26+,28-,29-;;;/m1.../s1
SMILES:  CC(CCC(C)C(C)(C)C)C1CCC2C1(CCC3C2CC(C4C3(CC(C(C4)OS(=O)(=O)[O-])OS(=O)(=O)[O-])C)OS(=O)(=O)[O-])C.[Na+].[Na+].[Na+]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL445456
PubChem CID:   10101618
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0003567] Ergostane steroids

*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
NPO33160 aka sp. Species n.a. n.a. n.a. Micronesian n.a. PMID[12762808]
NPO29375 Penicillium thomii Species Aspergillaceae Eukaryota n.a. Lazurnaya Bay, the Sea of Japan n.a. PMID[24852445]
NPO29375 Penicillium thomii Species Aspergillaceae Eukaryota n.a. isolated from superficial mycobiota of the brown alga Sargassum miyabei (Lazurnaya Bay, the Sea of Japan) n.a. PMID[24852445]
NPO33623 Penicillium lividum Species Aspergillaceae Eukaryota n.a. Lazurnaya Bay, the Sea of Japan n.a. PMID[24852445]
NPO33623 Penicillium lividum Species Aspergillaceae Eukaryota n.a. isolated from superficial mycobiota of the brown alga Sargassum miyabei (Lazurnaya Bay, the Sea of Japan) n.a. PMID[24852445]
NPO29375 Penicillium thomii Species Aspergillaceae 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
NPT4015 Individual Protein Matrix metalloproteinase 14 Homo sapiens IC50 = 19.0 ug.mL-1 PMID[495758]
NPT1560 Protein Complex Cyclin-dependent kinase 4/cyclin D1 Homo sapiens IC50 = 9.5 ug.mL-1 PMID[495759]
NPT2 Others Unspecified IC50 = 130000.0 nM PMID[495760]

☑ 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 NPC473552 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
1.0 High Similarity NPC323900
1.0 High Similarity NPC477821
1.0 High Similarity NPC477823
1.0 High Similarity NPC324984
1.0 High Similarity NPC477822
0.9394 High Similarity NPC475172
0.9155 High Similarity NPC473916
0.9155 High Similarity NPC477602
0.9155 High Similarity NPC477601
0.9091 High Similarity NPC477603
0.8857 High Similarity NPC478103
0.8493 Intermediate Similarity NPC478105
0.8462 Intermediate Similarity NPC469878
0.8356 Intermediate Similarity NPC478130
0.8333 Intermediate Similarity NPC478054
0.831 Intermediate Similarity NPC66407
0.8243 Intermediate Similarity NPC196136
0.8243 Intermediate Similarity NPC158208
0.8243 Intermediate Similarity NPC243027
0.8219 Intermediate Similarity NPC470610
0.8194 Intermediate Similarity NPC63588
0.8194 Intermediate Similarity NPC251201
0.8194 Intermediate Similarity NPC232925
0.8133 Intermediate Similarity NPC163597
0.8108 Intermediate Similarity NPC48795
0.8108 Intermediate Similarity NPC192501
0.8108 Intermediate Similarity NPC10476
0.8108 Intermediate Similarity NPC228994
0.8082 Intermediate Similarity NPC187471
0.8082 Intermediate Similarity NPC470071
0.8082 Intermediate Similarity NPC127094
0.8082 Intermediate Similarity NPC252182
0.8082 Intermediate Similarity NPC1340
0.8056 Intermediate Similarity NPC477820
0.8052 Intermediate Similarity NPC474132
0.8026 Intermediate Similarity NPC105208
0.8026 Intermediate Similarity NPC128951
0.8026 Intermediate Similarity NPC302578
0.8026 Intermediate Similarity NPC192046
0.8026 Intermediate Similarity NPC477227
0.8025 Intermediate Similarity NPC478094
0.8 Intermediate Similarity NPC320824
0.8 Intermediate Similarity NPC317242
0.7975 Intermediate Similarity NPC477599
0.7973 Intermediate Similarity NPC153719
0.7945 Intermediate Similarity NPC192192
0.7927 Intermediate Similarity NPC477600
0.7922 Intermediate Similarity NPC147993
0.7922 Intermediate Similarity NPC478128
0.7922 Intermediate Similarity NPC67657
0.7922 Intermediate Similarity NPC18857
0.7867 Intermediate Similarity NPC304499
0.7808 Intermediate Similarity NPC129829
0.7808 Intermediate Similarity NPC107919
0.7808 Intermediate Similarity NPC470833
0.7808 Intermediate Similarity NPC254037
0.7792 Intermediate Similarity NPC185915
0.7792 Intermediate Similarity NPC64081
0.7792 Intermediate Similarity NPC474574
0.7714 Intermediate Similarity NPC114891
0.7703 Intermediate Similarity NPC231945
0.7671 Intermediate Similarity NPC472741
0.7639 Intermediate Similarity NPC142712
0.7639 Intermediate Similarity NPC44122
0.7625 Intermediate Similarity NPC473534
0.76 Intermediate Similarity NPC109457
0.76 Intermediate Similarity NPC100586
0.76 Intermediate Similarity NPC157422
0.7595 Intermediate Similarity NPC287452
0.7595 Intermediate Similarity NPC81074
0.7595 Intermediate Similarity NPC477287
0.7595 Intermediate Similarity NPC477282
0.7571 Intermediate Similarity NPC148174
0.7571 Intermediate Similarity NPC71460
0.7571 Intermediate Similarity NPC218585
0.7568 Intermediate Similarity NPC241085
0.7568 Intermediate Similarity NPC299948
0.7568 Intermediate Similarity NPC470830
0.7564 Intermediate Similarity NPC11907
0.7564 Intermediate Similarity NPC133596
0.7534 Intermediate Similarity NPC473230
0.7534 Intermediate Similarity NPC48079
0.7534 Intermediate Similarity NPC475884
0.7532 Intermediate Similarity NPC270306
0.7532 Intermediate Similarity NPC91387
0.7532 Intermediate Similarity NPC231680
0.7531 Intermediate Similarity NPC477284
0.7531 Intermediate Similarity NPC202688
0.7531 Intermediate Similarity NPC154043
0.7531 Intermediate Similarity NPC60018
0.7531 Intermediate Similarity NPC121121
0.75 Intermediate Similarity NPC16449
0.75 Intermediate Similarity NPC474380
0.75 Intermediate Similarity NPC41577
0.75 Intermediate Similarity NPC473276
0.7471 Intermediate Similarity NPC476669
0.7467 Intermediate Similarity NPC282454
0.7439 Intermediate Similarity NPC85095
0.7439 Intermediate Similarity NPC216420
0.7439 Intermediate Similarity NPC211135
0.7386 Intermediate Similarity NPC475325
0.7375 Intermediate Similarity NPC269333
0.7375 Intermediate Similarity NPC476176
0.7368 Intermediate Similarity NPC131506
0.7368 Intermediate Similarity NPC126642
0.7368 Intermediate Similarity NPC157777
0.7361 Intermediate Similarity NPC159654
0.7361 Intermediate Similarity NPC69149
0.7361 Intermediate Similarity NPC167995
0.7361 Intermediate Similarity NPC281540
0.7361 Intermediate Similarity NPC118937
0.7356 Intermediate Similarity NPC473637
0.7356 Intermediate Similarity NPC476668
0.7349 Intermediate Similarity NPC255882
0.7349 Intermediate Similarity NPC478102
0.7342 Intermediate Similarity NPC212453
0.7342 Intermediate Similarity NPC476233
0.7333 Intermediate Similarity NPC99264
0.7317 Intermediate Similarity NPC470611
0.7317 Intermediate Similarity NPC286719
0.7317 Intermediate Similarity NPC475388
0.7317 Intermediate Similarity NPC477286
0.7297 Intermediate Similarity NPC63190
0.7284 Intermediate Similarity NPC78545
0.7284 Intermediate Similarity NPC71535
0.7273 Intermediate Similarity NPC473238
0.7273 Intermediate Similarity NPC472341
0.7262 Intermediate Similarity NPC266651
0.7262 Intermediate Similarity NPC232044
0.7262 Intermediate Similarity NPC273290
0.726 Intermediate Similarity NPC472946
0.725 Intermediate Similarity NPC329117
0.725 Intermediate Similarity NPC80089
0.725 Intermediate Similarity NPC34046
0.725 Intermediate Similarity NPC171426
0.725 Intermediate Similarity NPC324700
0.725 Intermediate Similarity NPC224802
0.725 Intermediate Similarity NPC471045
0.725 Intermediate Similarity NPC477817
0.725 Intermediate Similarity NPC477819
0.725 Intermediate Similarity NPC475337
0.725 Intermediate Similarity NPC471769
0.7229 Intermediate Similarity NPC470070
0.7229 Intermediate Similarity NPC477285
0.7229 Intermediate Similarity NPC111582
0.7222 Intermediate Similarity NPC236099
0.7222 Intermediate Similarity NPC209686
0.7222 Intermediate Similarity NPC249078
0.7222 Intermediate Similarity NPC473287
0.72 Intermediate Similarity NPC474756
0.7195 Intermediate Similarity NPC190940
0.7195 Intermediate Similarity NPC469745
0.7195 Intermediate Similarity NPC73515
0.7191 Intermediate Similarity NPC473503
0.7179 Intermediate Similarity NPC308440
0.7179 Intermediate Similarity NPC472503
0.7179 Intermediate Similarity NPC475458
0.7176 Intermediate Similarity NPC477283
0.7176 Intermediate Similarity NPC471240
0.7176 Intermediate Similarity NPC477604
0.7176 Intermediate Similarity NPC121981
0.716 Intermediate Similarity NPC220379
0.716 Intermediate Similarity NPC201276
0.716 Intermediate Similarity NPC80891
0.7143 Intermediate Similarity NPC195530
0.7143 Intermediate Similarity NPC477226
0.7143 Intermediate Similarity NPC473279
0.7143 Intermediate Similarity NPC8004
0.7143 Intermediate Similarity NPC476735
0.7143 Intermediate Similarity NPC127283
0.7143 Intermediate Similarity NPC227260
0.7126 Intermediate Similarity NPC20822
0.7126 Intermediate Similarity NPC473472
0.7125 Intermediate Similarity NPC202540
0.7125 Intermediate Similarity NPC207010
0.7125 Intermediate Similarity NPC317913
0.7111 Intermediate Similarity NPC469710
0.7108 Intermediate Similarity NPC296734
0.7093 Intermediate Similarity NPC186145
0.7093 Intermediate Similarity NPC474657
0.7093 Intermediate Similarity NPC263802
0.7093 Intermediate Similarity NPC475313
0.7093 Intermediate Similarity NPC478104
0.7093 Intermediate Similarity NPC43912
0.7093 Intermediate Similarity NPC140446
0.7089 Intermediate Similarity NPC3403
0.7089 Intermediate Similarity NPC103822
0.7073 Intermediate Similarity NPC475679
0.7073 Intermediate Similarity NPC470609
0.7067 Intermediate Similarity NPC204233
0.7065 Intermediate Similarity NPC473638
0.7059 Intermediate Similarity NPC290612
0.7051 Intermediate Similarity NPC232112
0.7045 Intermediate Similarity NPC223143
0.7037 Intermediate Similarity NPC102708
0.7037 Intermediate Similarity NPC301707
0.7037 Intermediate Similarity NPC31828
0.7027 Intermediate Similarity NPC260116
0.7027 Intermediate Similarity NPC243469
0.7027 Intermediate Similarity NPC475943

  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 NPC473552 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
0.7808 Intermediate Similarity NPD4267 Clinical (unspecified phase)
0.725 Intermediate Similarity NPD6118 Approved
0.725 Intermediate Similarity NPD6697 Approved
0.725 Intermediate Similarity NPD6114 Approved
0.725 Intermediate Similarity NPD6115 Approved
0.7125 Intermediate Similarity NPD6116 Phase 1
0.7013 Intermediate Similarity NPD4787 Phase 1
0.7 Intermediate Similarity NPD6117 Approved
0.6923 Remote Similarity NPD4809 Clinical (unspecified phase)
0.6923 Remote Similarity NPD4808 Clinical (unspecified phase)
0.6875 Remote Similarity NPD3703 Phase 2
0.6867 Remote Similarity NPD6928 Phase 2
0.6867 Remote Similarity NPD7525 Registered
0.6854 Remote Similarity NPD6700 Approved
0.6854 Remote Similarity NPD6701 Clinical (unspecified phase)
0.6829 Remote Similarity NPD5364 Discontinued
0.6778 Remote Similarity NPD6703 Approved
0.6778 Remote Similarity NPD6702 Approved
0.675 Remote Similarity NPD6113 Clinical (unspecified phase)
0.6667 Remote Similarity NPD3699 Clinical (unspecified phase)
0.6667 Remote Similarity NPD3700 Clinical (unspecified phase)
0.6538 Remote Similarity NPD5360 Phase 3
0.6538 Remote Similarity NPD5361 Clinical (unspecified phase)
0.6522 Remote Similarity NPD8171 Discontinued
0.6404 Remote Similarity NPD8308 Discontinued
0.6375 Remote Similarity NPD4244 Approved
0.6375 Remote Similarity NPD4245 Approved
0.6375 Remote Similarity NPD4789 Approved
0.6296 Remote Similarity NPD5777 Approved
0.625 Remote Similarity NPD3698 Phase 2
0.6154 Remote Similarity NPD3171 Clinical (unspecified phase)
0.6111 Remote Similarity NPD7520 Clinical (unspecified phase)
0.6098 Remote Similarity NPD4758 Discontinued
0.6098 Remote Similarity NPD6081 Approved
0.6082 Remote Similarity NPD7919 Phase 3
0.6082 Remote Similarity NPD7920 Phase 3
0.6071 Remote Similarity NPD6942 Approved
0.6071 Remote Similarity NPD7339 Approved
0.6064 Remote Similarity NPD8034 Phase 2
0.6064 Remote Similarity NPD8035 Phase 2
0.6047 Remote Similarity NPD3671 Phase 1
0.6042 Remote Similarity NPD7991 Discontinued
0.6026 Remote Similarity NPD371 Approved
0.602 Remote Similarity NPD8088 Phase 1
0.6 Remote Similarity NPD3668 Phase 3
0.5976 Remote Similarity NPD2254 Approved
0.5976 Remote Similarity NPD2687 Approved
0.5976 Remote Similarity NPD2686 Approved
0.5926 Remote Similarity NPD6705 Phase 1
0.5882 Remote Similarity NPD8170 Clinical (unspecified phase)
0.5875 Remote Similarity NPD4224 Phase 2
0.5814 Remote Similarity NPD3701 Clinical (unspecified phase)
0.58 Remote Similarity NPD8418 Phase 2
0.5795 Remote Similarity NPD7645 Phase 2
0.5733 Remote Similarity NPD586 Phase 1
0.573 Remote Similarity NPD4748 Discontinued
0.57 Remote Similarity NPD7638 Approved
0.5698 Remote Similarity NPD3702 Approved
0.5684 Remote Similarity NPD5328 Approved
0.5652 Remote Similarity NPD7338 Clinical (unspecified phase)
0.5652 Remote Similarity NPD4786 Approved
0.5644 Remote Similarity NPD7639 Approved
0.5644 Remote Similarity NPD7640 Approved
0.5638 Remote Similarity NPD7524 Approved
0.5638 Remote Similarity NPD4751 Clinical (unspecified phase)
0.5632 Remote Similarity NPD6933 Approved
0.5618 Remote Similarity NPD6929 Approved
0.5606 Remote Similarity NPD1460 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