Structure

Physi-Chem Properties

Molecular Weight:  182.17
Volume:  207.786
LogP:  3.149
LogD:  2.631
LogS:  -3.161
# Rotatable Bonds:  0
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.61
Synthetic Accessibility Score:  3.801
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.452
MDCK Permeability:  1.8047825506073423e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.781
30% Bioavailability (F30%):  0.92

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.343
Plasma Protein Binding (PPB):  91.07355499267578%
Volume Distribution (VD):  1.171
Pgp-substrate:  7.269608020782471%

ADMET: Metabolism

CYP1A2-inhibitor:  0.374
CYP1A2-substrate:  0.528
CYP2C19-inhibitor:  0.351
CYP2C19-substrate:  0.898
CYP2C9-inhibitor:  0.18
CYP2C9-substrate:  0.298
CYP2D6-inhibitor:  0.028
CYP2D6-substrate:  0.363
CYP3A4-inhibitor:  0.421
CYP3A4-substrate:  0.305

ADMET: Excretion

Clearance (CL):  9.438
Half-life (T1/2):  0.16

ADMET: Toxicity

hERG Blockers:  0.093
Human Hepatotoxicity (H-HT):  0.061
Drug-inuced Liver Injury (DILI):  0.05
AMES Toxicity:  0.018
Rat Oral Acute Toxicity:  0.064
Maximum Recommended Daily Dose:  0.056
Skin Sensitization:  0.826
Carcinogencity:  0.493
Eye Corrosion:  0.951
Eye Irritation:  0.975
Respiratory Toxicity:  0.928

Download Data

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

  Natural Product: NPC14552

Natural Product ID:  NPC14552
Common Name*:   geosmin
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  JLPUXFOGCDVKGO-TUAOUCFPSA-N
Standard InCHI:  InChI=1S/C12H22O/c1-10-6-5-8-11(2)7-3-4-9-12(10,11)13/h10,13H,3-9H2,1-2H3/t10-,11+,12-/m0/s1
SMILES:  C[C@H]1CCC[C@@]2([C@]1(O)CCCC2)C
Synthetic Gene Cluster:   BGC0001181;
ChEMBL Identifier:   n.a.
PubChem CID:   29746
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001670] Tertiary alcohols

*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
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. DOI[10.1021/jf00055a023]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. seed n.a. PMID[11539687]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. PMID[12713418]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. PMID[21080643]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. husk n.a. PMID[21574561]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. leaf n.a. PMID[21574561]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. seed n.a. PMID[23292602]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. PMID[29762032]
NPO41816 Streptomyces spp. [n.a.] Strain Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[30196100]
NPO41816 Streptomyces spp. [n.a.] Strain Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[32808679]
NPO41816 Streptomyces spp. [n.a.] Strain Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[33974270]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. pollen n.a. PMID[8987503]
NPO15810 Zea mays Species Poaceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Pollen Or Spore n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Seed Essent. Oil n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Silk Essent. Oil n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Silk Stigma Style n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Cob n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Husk Essent. Oil n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15810 Zea mays Species Poaceae 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
NPO15810 NPC14552 Raw Husk Essent. Oil 200 200 200 mg/100g Database [DUKE]
NPO15810 NPC14552 Raw Seed Essent. Oil 400 400 400 mg/100g Database [DUKE]

☑ 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
NPT442 Individual Protein Ferritin light chain Equus caballus Potency = 8912.5 nM PMID[573901]
NPT49 Individual Protein DNA-(apurinic or apyrimidinic site) lyase Homo sapiens Potency n.a. 398.1 nM PMID[573901]

☑ 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 NPC14552 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
0.8776 High Similarity NPC102336
0.8776 High Similarity NPC36002
0.8723 High Similarity NPC316035
0.8269 Intermediate Similarity NPC3025
0.8113 Intermediate Similarity NPC135438
0.8113 Intermediate Similarity NPC236588
0.7963 Intermediate Similarity NPC474769
0.7963 Intermediate Similarity NPC189290
0.7959 Intermediate Similarity NPC294858
0.7925 Intermediate Similarity NPC264779
0.7885 Intermediate Similarity NPC32222
0.7885 Intermediate Similarity NPC202146
0.7872 Intermediate Similarity NPC313795
0.7818 Intermediate Similarity NPC95958
0.7736 Intermediate Similarity NPC471269
0.7636 Intermediate Similarity NPC162685
0.7547 Intermediate Similarity NPC53209
0.74 Intermediate Similarity NPC314087
0.7347 Intermediate Similarity NPC108441
0.7347 Intermediate Similarity NPC77550
0.7321 Intermediate Similarity NPC47663
0.7288 Intermediate Similarity NPC101128
0.7273 Intermediate Similarity NPC179024
0.7273 Intermediate Similarity NPC39068
0.7273 Intermediate Similarity NPC328441
0.7241 Intermediate Similarity NPC41160
0.72 Intermediate Similarity NPC176309
0.72 Intermediate Similarity NPC147343
0.72 Intermediate Similarity NPC84030
0.72 Intermediate Similarity NPC287550
0.72 Intermediate Similarity NPC223468
0.72 Intermediate Similarity NPC198540
0.7167 Intermediate Similarity NPC19311
0.7167 Intermediate Similarity NPC80463
0.7167 Intermediate Similarity NPC260116
0.7167 Intermediate Similarity NPC258595
0.7167 Intermediate Similarity NPC64123
0.7167 Intermediate Similarity NPC230047
0.7119 Intermediate Similarity NPC292419
0.7119 Intermediate Similarity NPC209686
0.7119 Intermediate Similarity NPC236099
0.7119 Intermediate Similarity NPC249078
0.7119 Intermediate Similarity NPC290791
0.7018 Intermediate Similarity NPC475515
0.7018 Intermediate Similarity NPC87296
0.7018 Intermediate Similarity NPC215671
0.7018 Intermediate Similarity NPC476735
0.7 Intermediate Similarity NPC144650
0.6949 Remote Similarity NPC148174
0.6949 Remote Similarity NPC185547
0.6949 Remote Similarity NPC218585
0.6949 Remote Similarity NPC95804
0.6949 Remote Similarity NPC71460
0.6939 Remote Similarity NPC144891
0.6935 Remote Similarity NPC185874
0.6935 Remote Similarity NPC88454
0.6935 Remote Similarity NPC476928
0.6935 Remote Similarity NPC48079
0.6935 Remote Similarity NPC63190
0.6935 Remote Similarity NPC41542
0.6935 Remote Similarity NPC139207
0.6935 Remote Similarity NPC269077
0.6935 Remote Similarity NPC117607
0.6935 Remote Similarity NPC101307
0.6935 Remote Similarity NPC253303
0.6923 Remote Similarity NPC95969
0.6923 Remote Similarity NPC127997
0.6885 Remote Similarity NPC473276
0.6885 Remote Similarity NPC243469
0.6885 Remote Similarity NPC190827
0.6885 Remote Similarity NPC172613
0.6885 Remote Similarity NPC474380
0.6885 Remote Similarity NPC282619
0.6885 Remote Similarity NPC208198
0.6885 Remote Similarity NPC41577
0.6885 Remote Similarity NPC475943
0.6885 Remote Similarity NPC472946
0.6885 Remote Similarity NPC11555
0.6885 Remote Similarity NPC2728
0.6885 Remote Similarity NPC60837
0.6833 Remote Similarity NPC114891
0.6825 Remote Similarity NPC474756
0.6825 Remote Similarity NPC244790
0.6825 Remote Similarity NPC475893
0.6825 Remote Similarity NPC94192
0.6825 Remote Similarity NPC472741
0.6825 Remote Similarity NPC2648
0.6786 Remote Similarity NPC300189
0.6774 Remote Similarity NPC142712
0.6774 Remote Similarity NPC44122
0.6774 Remote Similarity NPC473929
0.6774 Remote Similarity NPC476406
0.6774 Remote Similarity NPC103734
0.6739 Remote Similarity NPC177022
0.6721 Remote Similarity NPC118937
0.6721 Remote Similarity NPC167995
0.6721 Remote Similarity NPC159654
0.6721 Remote Similarity NPC69149
0.6721 Remote Similarity NPC281540
0.6721 Remote Similarity NPC94897
0.6721 Remote Similarity NPC68656
0.6719 Remote Similarity NPC196197
0.6719 Remote Similarity NPC210323
0.6719 Remote Similarity NPC470833
0.6719 Remote Similarity NPC299948
0.6719 Remote Similarity NPC66407
0.6719 Remote Similarity NPC107919
0.6719 Remote Similarity NPC254037
0.6719 Remote Similarity NPC470830
0.6719 Remote Similarity NPC476431
0.6719 Remote Similarity NPC129829
0.6719 Remote Similarity NPC241085
0.6667 Remote Similarity NPC472984
0.6667 Remote Similarity NPC307022
0.6667 Remote Similarity NPC473230
0.6667 Remote Similarity NPC79576
0.6667 Remote Similarity NPC160261
0.6667 Remote Similarity NPC469759
0.6667 Remote Similarity NPC475884
0.6667 Remote Similarity NPC282694
0.6667 Remote Similarity NPC204233
0.6667 Remote Similarity NPC194208
0.6615 Remote Similarity NPC283316
0.6615 Remote Similarity NPC231945
0.6615 Remote Similarity NPC192192
0.6615 Remote Similarity NPC282454
0.6613 Remote Similarity NPC469791
0.66 Remote Similarity NPC302939
0.66 Remote Similarity NPC287331
0.6562 Remote Similarity NPC478228
0.6562 Remote Similarity NPC276616
0.6562 Remote Similarity NPC469987
0.6562 Remote Similarity NPC473225
0.6562 Remote Similarity NPC245795
0.6557 Remote Similarity NPC81615
0.6552 Remote Similarity NPC29976
0.6552 Remote Similarity NPC150713
0.6515 Remote Similarity NPC131506
0.6515 Remote Similarity NPC470071
0.6515 Remote Similarity NPC8004
0.6515 Remote Similarity NPC127283
0.6515 Remote Similarity NPC127094
0.6515 Remote Similarity NPC252182
0.6515 Remote Similarity NPC167706
0.6515 Remote Similarity NPC109457
0.6515 Remote Similarity NPC195530
0.6515 Remote Similarity NPC1340
0.6515 Remote Similarity NPC157422
0.6515 Remote Similarity NPC473279
0.6515 Remote Similarity NPC157777
0.6515 Remote Similarity NPC187471
0.6515 Remote Similarity NPC100586
0.6515 Remote Similarity NPC247195
0.6508 Remote Similarity NPC475897
0.6508 Remote Similarity NPC279434
0.65 Remote Similarity NPC204173
0.65 Remote Similarity NPC135648
0.6491 Remote Similarity NPC218525
0.6462 Remote Similarity NPC477820
0.6462 Remote Similarity NPC9942
0.6458 Remote Similarity NPC221022
0.6452 Remote Similarity NPC128608
0.6452 Remote Similarity NPC219940
0.6429 Remote Similarity NPC161473
0.6418 Remote Similarity NPC81759
0.6418 Remote Similarity NPC95165
0.6418 Remote Similarity NPC153719
0.6418 Remote Similarity NPC253805
0.6418 Remote Similarity NPC472341
0.6418 Remote Similarity NPC473238
0.6415 Remote Similarity NPC100445
0.6406 Remote Similarity NPC263161
0.6364 Remote Similarity NPC475728
0.6364 Remote Similarity NPC63588
0.6364 Remote Similarity NPC251201
0.6364 Remote Similarity NPC232925
0.6364 Remote Similarity NPC45296
0.6364 Remote Similarity NPC163020
0.6349 Remote Similarity NPC476737
0.6349 Remote Similarity NPC27243
0.6349 Remote Similarity NPC474768
0.6333 Remote Similarity NPC185116
0.6324 Remote Similarity NPC477508
0.6324 Remote Similarity NPC10476
0.6324 Remote Similarity NPC74639
0.6324 Remote Similarity NPC475458
0.6324 Remote Similarity NPC470151
0.6324 Remote Similarity NPC228994
0.6324 Remote Similarity NPC162164
0.6324 Remote Similarity NPC38426
0.6324 Remote Similarity NPC22134
0.6324 Remote Similarity NPC237510
0.6324 Remote Similarity NPC201048
0.6324 Remote Similarity NPC475793
0.6324 Remote Similarity NPC192501
0.6324 Remote Similarity NPC476366
0.6324 Remote Similarity NPC304499
0.6308 Remote Similarity NPC266578
0.6308 Remote Similarity NPC2568
0.6308 Remote Similarity NPC260319

  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 NPC14552 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
0.7347 Intermediate Similarity NPD386 Approved
0.7347 Intermediate Similarity NPD388 Approved
0.72 Intermediate Similarity NPD385 Approved
0.72 Intermediate Similarity NPD384 Approved
0.6719 Remote Similarity NPD4267 Clinical (unspecified phase)
0.6613 Remote Similarity NPD3171 Clinical (unspecified phase)
0.66 Remote Similarity NPD367 Approved
0.6562 Remote Similarity NPD5361 Clinical (unspecified phase)
0.6562 Remote Similarity NPD5360 Phase 3
0.6508 Remote Similarity NPD4224 Phase 2
0.6364 Remote Similarity NPD4787 Phase 1
0.6269 Remote Similarity NPD4243 Approved
0.6269 Remote Similarity NPD4758 Discontinued
0.6212 Remote Similarity NPD3700 Clinical (unspecified phase)
0.6212 Remote Similarity NPD3698 Phase 2
0.6212 Remote Similarity NPD3699 Clinical (unspecified phase)
0.6119 Remote Similarity NPD4244 Approved
0.6119 Remote Similarity NPD4789 Approved
0.6119 Remote Similarity NPD4245 Approved
0.6087 Remote Similarity NPD4784 Approved
0.6087 Remote Similarity NPD4785 Approved
0.6061 Remote Similarity NPD6705 Phase 1
0.6029 Remote Similarity NPD4809 Clinical (unspecified phase)
0.6029 Remote Similarity NPD4808 Clinical (unspecified phase)
0.6029 Remote Similarity NPD6081 Approved
0.6 Remote Similarity NPD5275 Approved
0.6 Remote Similarity NPD4190 Phase 3
0.6 Remote Similarity NPD3703 Phase 2
0.6 Remote Similarity NPD3702 Approved
0.5938 Remote Similarity NPD371 Approved
0.5915 Remote Similarity NPD6117 Approved
0.5857 Remote Similarity NPD6926 Approved
0.5857 Remote Similarity NPD6113 Clinical (unspecified phase)
0.5857 Remote Similarity NPD6924 Approved
0.5833 Remote Similarity NPD6116 Phase 1
0.5811 Remote Similarity NPD7525 Registered
0.5775 Remote Similarity NPD7339 Approved
0.5775 Remote Similarity NPD6942 Approved
0.5769 Remote Similarity NPD1462 Approved
0.5763 Remote Similarity NPD615 Clinical (unspecified phase)
0.5753 Remote Similarity NPD5364 Discontinued
0.5753 Remote Similarity NPD6697 Approved
0.5753 Remote Similarity NPD6115 Approved
0.5753 Remote Similarity NPD6118 Approved
0.5753 Remote Similarity NPD6114 Approved
0.5741 Remote Similarity NPD634 Phase 3
0.5735 Remote Similarity NPD6923 Approved
0.5735 Remote Similarity NPD6922 Approved
0.5694 Remote Similarity NPD3701 Clinical (unspecified phase)
0.5694 Remote Similarity NPD6933 Approved
0.5686 Remote Similarity NPD1460 Approved
0.5676 Remote Similarity NPD7645 Phase 2
0.5676 Remote Similarity NPD4195 Approved
0.5652 Remote Similarity NPD7144 Approved
0.5652 Remote Similarity NPD7143 Approved
0.5634 Remote Similarity NPD1810 Approved
0.5634 Remote Similarity NPD1811 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