Structure

Physi-Chem Properties

Molecular Weight:  146.09
Volume:  147.443
LogP:  -0.5
LogD:  -0.807
LogS:  0.424
# Rotatable Bonds:  0
TPSA:  60.69
# H-Bond Aceptor:  3
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.431
Synthetic Accessibility Score:  3.779
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.035
MDCK Permeability:  9.951434913091362e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.988
Human Intestinal Absorption (HIA):  0.035
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.087

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.175
Plasma Protein Binding (PPB):  10.522361755371094%
Volume Distribution (VD):  1.417
Pgp-substrate:  74.77626037597656%

ADMET: Metabolism

CYP1A2-inhibitor:  0.025
CYP1A2-substrate:  0.111
CYP2C19-inhibitor:  0.018
CYP2C19-substrate:  0.742
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.763
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.124
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.091

ADMET: Excretion

Clearance (CL):  5.099
Half-life (T1/2):  0.741

ADMET: Toxicity

hERG Blockers:  0.06
Human Hepatotoxicity (H-HT):  0.11
Drug-inuced Liver Injury (DILI):  0.095
AMES Toxicity:  0.072
Rat Oral Acute Toxicity:  0.122
Maximum Recommended Daily Dose:  0.027
Skin Sensitization:  0.775
Carcinogencity:  0.124
Eye Corrosion:  0.925
Eye Irritation:  0.986
Respiratory Toxicity:  0.747

Download Data

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

  Natural Product: NPC244869

Natural Product ID:  NPC244869
Common Name*:   Ampelomin D
IUPAC Name:   (1S,2R,4R,5S)-5-methylcyclohexane-1,2,4-triol
Synonyms:   Ampelomin D
Standard InCHIKey:  DKCGTIMNFPMKNS-BNHYGAARSA-N
Standard InCHI:  InChI=1S/C7H14O3/c1-4-2-6(9)7(10)3-5(4)8/h4-10H,2-3H2,1H3/t4-,5+,6-,7+/m0/s1
SMILES:  O[C@@H]1C[C@@H](O)[C@H](C[C@@H]1C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL550966
PubChem CID:   25243399
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001661] Secondary alcohols
            • [CHEMONTID:0002647] Cyclohexanols

*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
NPO32705 ampelomyces sp. Species Leptosphaeriaceae Eukaryota n.a. n.a. n.a. PMID[19193024]

☑ 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
NPT2 Others Unspecified IC50 > 10000000.0 nM PMID[459050]

☑ 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 NPC244869 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 NPC300235
1.0 High Similarity NPC476149
1.0 High Similarity NPC476136
0.8889 High Similarity NPC476209
0.8545 High Similarity NPC182903
0.8136 Intermediate Similarity NPC94897
0.746 Intermediate Similarity NPC179823
0.7347 Intermediate Similarity NPC227707
0.7347 Intermediate Similarity NPC111882
0.7347 Intermediate Similarity NPC102981
0.7347 Intermediate Similarity NPC88278
0.7347 Intermediate Similarity NPC99573
0.7288 Intermediate Similarity NPC47663
0.7167 Intermediate Similarity NPC185116
0.7115 Intermediate Similarity NPC207656
0.7115 Intermediate Similarity NPC107091
0.7115 Intermediate Similarity NPC240994
0.7069 Intermediate Similarity NPC471269
0.7059 Intermediate Similarity NPC470151
0.697 Remote Similarity NPC470833
0.6964 Remote Similarity NPC307022
0.6923 Remote Similarity NPC53879
0.6923 Remote Similarity NPC57788
0.6852 Remote Similarity NPC84030
0.6852 Remote Similarity NPC147343
0.6852 Remote Similarity NPC176309
0.6852 Remote Similarity NPC223468
0.6852 Remote Similarity NPC198540
0.6852 Remote Similarity NPC287550
0.6812 Remote Similarity NPC228994
0.6812 Remote Similarity NPC192501
0.6812 Remote Similarity NPC10476
0.6721 Remote Similarity NPC87296
0.6721 Remote Similarity NPC475515
0.6721 Remote Similarity NPC215671
0.6714 Remote Similarity NPC243027
0.6714 Remote Similarity NPC158208
0.6714 Remote Similarity NPC196136
0.6667 Remote Similarity NPC147993
0.6604 Remote Similarity NPC144891
0.6571 Remote Similarity NPC166250
0.6545 Remote Similarity NPC88638
0.6545 Remote Similarity NPC314613
0.6528 Remote Similarity NPC302578
0.6528 Remote Similarity NPC105208
0.6528 Remote Similarity NPC192046
0.6528 Remote Similarity NPC477227
0.6528 Remote Similarity NPC128951
0.6486 Remote Similarity NPC471266
0.6486 Remote Similarity NPC95124
0.6479 Remote Similarity NPC244539
0.6438 Remote Similarity NPC18857
0.6438 Remote Similarity NPC67657
0.6429 Remote Similarity NPC95165
0.6418 Remote Similarity NPC476650
0.64 Remote Similarity NPC471270
0.64 Remote Similarity NPC470156
0.6389 Remote Similarity NPC313762
0.6389 Remote Similarity NPC163597
0.6364 Remote Similarity NPC77550
0.6364 Remote Similarity NPC108441
0.6351 Remote Similarity NPC269333
0.6333 Remote Similarity NPC53209
0.6327 Remote Similarity NPC192065
0.6327 Remote Similarity NPC66052
0.6327 Remote Similarity NPC325034
0.6327 Remote Similarity NPC86412
0.6327 Remote Similarity NPC293908
0.6324 Remote Similarity NPC474756
0.6324 Remote Similarity NPC469987
0.6316 Remote Similarity NPC325822
0.6316 Remote Similarity NPC224987
0.6316 Remote Similarity NPC470155
0.6316 Remote Similarity NPC477446
0.6316 Remote Similarity NPC477447
0.6316 Remote Similarity NPC61270
0.6301 Remote Similarity NPC185915
0.629 Remote Similarity NPC236588
0.6267 Remote Similarity NPC186588
0.6267 Remote Similarity NPC16449
0.6267 Remote Similarity NPC236707
0.625 Remote Similarity NPC475412
0.625 Remote Similarity NPC472952
0.625 Remote Similarity NPC472950
0.625 Remote Similarity NPC317242
0.6234 Remote Similarity NPC478054
0.6234 Remote Similarity NPC241959
0.6232 Remote Similarity NPC234511
0.6216 Remote Similarity NPC43463
0.6216 Remote Similarity NPC52755
0.6216 Remote Similarity NPC272841
0.6197 Remote Similarity NPC470610
0.6184 Remote Similarity NPC470154
0.6184 Remote Similarity NPC211049
0.6176 Remote Similarity NPC204233
0.6164 Remote Similarity NPC136424
0.6154 Remote Similarity NPC95804
0.6154 Remote Similarity NPC320824
0.6154 Remote Similarity NPC185547
0.6154 Remote Similarity NPC172622
0.6143 Remote Similarity NPC471879
0.614 Remote Similarity NPC314087
0.6133 Remote Similarity NPC81074
0.6133 Remote Similarity NPC287452
0.6133 Remote Similarity NPC477282
0.6129 Remote Similarity NPC170780
0.6119 Remote Similarity NPC260116
0.6111 Remote Similarity NPC308489
0.6111 Remote Similarity NPC48795
0.6111 Remote Similarity NPC475458
0.6111 Remote Similarity NPC304499
0.6104 Remote Similarity NPC154043
0.6104 Remote Similarity NPC202688
0.6104 Remote Similarity NPC60018
0.6094 Remote Similarity NPC174485
0.6087 Remote Similarity NPC266578
0.6087 Remote Similarity NPC475893
0.6087 Remote Similarity NPC244790
0.6076 Remote Similarity NPC471267
0.6061 Remote Similarity NPC236099
0.6061 Remote Similarity NPC249078
0.6061 Remote Similarity NPC209686
0.6053 Remote Similarity NPC186594
0.6038 Remote Similarity NPC266553
0.6032 Remote Similarity NPC119425
0.6032 Remote Similarity NPC135438
0.6032 Remote Similarity NPC322148
0.6027 Remote Similarity NPC131584
0.6027 Remote Similarity NPC139765
0.6026 Remote Similarity NPC211135
0.6026 Remote Similarity NPC216420
0.6026 Remote Similarity NPC471987
0.6026 Remote Similarity NPC85095
0.6 Remote Similarity NPC477820
0.6 Remote Similarity NPC474215
0.6 Remote Similarity NPC475729
0.6 Remote Similarity NPC191345
0.6 Remote Similarity NPC321102
0.6 Remote Similarity NPC322803
0.6 Remote Similarity NPC107919
0.6 Remote Similarity NPC268633
0.6 Remote Similarity NPC325153
0.6 Remote Similarity NPC278465
0.6 Remote Similarity NPC252483
0.6 Remote Similarity NPC66407
0.5974 Remote Similarity NPC116320
0.5974 Remote Similarity NPC473257
0.5974 Remote Similarity NPC119922
0.5972 Remote Similarity NPC153719
0.597 Remote Similarity NPC476702
0.597 Remote Similarity NPC199937
0.5968 Remote Similarity NPC84824
0.5968 Remote Similarity NPC67508
0.5946 Remote Similarity NPC473916
0.5946 Remote Similarity NPC477602
0.5946 Remote Similarity NPC477601
0.5946 Remote Similarity NPC63958
0.5942 Remote Similarity NPC253303
0.5942 Remote Similarity NPC139207
0.5942 Remote Similarity NPC185874
0.5942 Remote Similarity NPC269077
0.5926 Remote Similarity NPC213658
0.5926 Remote Similarity NPC45833
0.5926 Remote Similarity NPC62202
0.5926 Remote Similarity NPC110365
0.5915 Remote Similarity NPC232925
0.5915 Remote Similarity NPC251201
0.5915 Remote Similarity NPC283316
0.5915 Remote Similarity NPC231945
0.5915 Remote Similarity NPC63588
0.5909 Remote Similarity NPC475807
0.5902 Remote Similarity NPC102336
0.5902 Remote Similarity NPC36002
0.5897 Remote Similarity NPC216800
0.5882 Remote Similarity NPC472946
0.5882 Remote Similarity NPC300442
0.5882 Remote Similarity NPC471200
0.5875 Remote Similarity NPC266651
0.5867 Remote Similarity NPC11907
0.5867 Remote Similarity NPC64081
0.5867 Remote Similarity NPC133596
0.5867 Remote Similarity NPC476719
0.5867 Remote Similarity NPC474574
0.5854 Remote Similarity NPC476379
0.5846 Remote Similarity NPC475968
0.5844 Remote Similarity NPC472951
0.5844 Remote Similarity NPC472943
0.5844 Remote Similarity NPC287749
0.5833 Remote Similarity NPC242992
0.5833 Remote Similarity NPC252182
0.5833 Remote Similarity NPC1340
0.5833 Remote Similarity NPC471271
0.5833 Remote Similarity NPC127094
0.5833 Remote Similarity NPC470071
0.5833 Remote Similarity NPC471268
0.5833 Remote Similarity NPC187471
0.5823 Remote Similarity NPC69953
0.5823 Remote Similarity NPC477978
0.5823 Remote Similarity NPC227170
0.5823 Remote Similarity NPC185605

  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 NPC244869 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
0.7833 Intermediate Similarity NPD371 Approved
0.7385 Intermediate Similarity NPD7532 Clinical (unspecified phase)
0.7347 Intermediate Similarity NPD8995 Clinical (unspecified phase)
0.7347 Intermediate Similarity NPD8996 Phase 3
0.7115 Intermediate Similarity NPD9218 Clinical (unspecified phase)
0.7115 Intermediate Similarity NPD9219 Approved
0.6852 Remote Similarity NPD384 Approved
0.6852 Remote Similarity NPD385 Approved
0.6364 Remote Similarity NPD386 Approved
0.6364 Remote Similarity NPD388 Approved
0.6327 Remote Similarity NPD9051 Approved
0.6327 Remote Similarity NPD9052 Approved
0.6327 Remote Similarity NPD9053 Approved
0.6316 Remote Similarity NPD9061 Clinical (unspecified phase)
0.6 Remote Similarity NPD4267 Clinical (unspecified phase)
0.5714 Remote Similarity NPD8814 Phase 3
0.5679 Remote Similarity NPD394 Phase 3

  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