Structure

Physi-Chem Properties

Molecular Weight:  278.19
Volume:  309.857
LogP:  4.124
LogD:  3.085
LogS:  -3.187
# Rotatable Bonds:  9
TPSA:  46.53
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.305
Synthetic Accessibility Score:  3.973
Fsp3:  0.706
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:  -4.637
MDCK Permeability:  2.3127520762500353e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.07
20% Bioavailability (F20%):  0.972
30% Bioavailability (F30%):  0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.935
Plasma Protein Binding (PPB):  96.39592742919922%
Volume Distribution (VD):  1.444
Pgp-substrate:  1.3464477062225342%

ADMET: Metabolism

CYP1A2-inhibitor:  0.822
CYP1A2-substrate:  0.408
CYP2C19-inhibitor:  0.7
CYP2C19-substrate:  0.647
CYP2C9-inhibitor:  0.389
CYP2C9-substrate:  0.934
CYP2D6-inhibitor:  0.146
CYP2D6-substrate:  0.089
CYP3A4-inhibitor:  0.813
CYP3A4-substrate:  0.112

ADMET: Excretion

Clearance (CL):  3.467
Half-life (T1/2):  0.158

ADMET: Toxicity

hERG Blockers:  0.02
Human Hepatotoxicity (H-HT):  0.184
Drug-inuced Liver Injury (DILI):  0.18
AMES Toxicity:  0.1
Rat Oral Acute Toxicity:  0.286
Maximum Recommended Daily Dose:  0.025
Skin Sensitization:  0.716
Carcinogencity:  0.472
Eye Corrosion:  0.728
Eye Irritation:  0.827
Respiratory Toxicity:  0.817

Download Data

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

  Natural Product: NPC150502

Natural Product ID:  NPC150502
Common Name*:   Lincomolide B
IUPAC Name:   (3E,4S,5S)-3-dodec-11-ynylidene-4-hydroxy-5-methyloxolan-2-one
Synonyms:  
Standard InCHIKey:  ZOHSBTYPSYCTIC-WPDDIUJQSA-N
Standard InCHI:  InChI=1S/C17H26O3/c1-3-4-5-6-7-8-9-10-11-12-13-15-16(18)14(2)20-17(15)19/h1,13-14,16,18H,4-12H2,2H3/b15-13+/t14-,16+/m0/s1
SMILES:  C#CCCCCCCCCC/C=C1/C(=O)O[C@H]([C@H]1O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL509648
PubChem CID:   11778320
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000050] Lactones
        • [CHEMONTID:0001245] Gamma butyrolactones

*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
NPO23473 Cinnamomum kotoense Species Lauraceae Eukaryota stem wood n.a. n.a. PMID[16180806]
NPO23473 Cinnamomum kotoense Species Lauraceae Eukaryota leaves n.a. n.a. PMID[16792412]
NPO23473 Cinnamomum kotoense Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[18489163]
NPO23473 Cinnamomum kotoense Species Lauraceae 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
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC = 10160.0 nM PMID[449794]

☑ 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 NPC150502 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
0.9079 High Similarity NPC301207
0.8961 High Similarity NPC125365
0.8961 High Similarity NPC51809
0.8961 High Similarity NPC49302
0.8961 High Similarity NPC474818
0.8961 High Similarity NPC176329
0.8875 High Similarity NPC11383
0.8875 High Similarity NPC310450
0.8875 High Similarity NPC474959
0.8875 High Similarity NPC475046
0.8846 High Similarity NPC473471
0.8846 High Similarity NPC279214
0.8846 High Similarity NPC221095
0.8831 High Similarity NPC209113
0.8831 High Similarity NPC127118
0.8765 High Similarity NPC229799
0.8765 High Similarity NPC286770
0.8765 High Similarity NPC284472
0.8228 Intermediate Similarity NPC161038
0.8049 Intermediate Similarity NPC99651
0.8025 Intermediate Similarity NPC275530
0.7901 Intermediate Similarity NPC205615
0.7901 Intermediate Similarity NPC256640
0.7901 Intermediate Similarity NPC16279
0.7889 Intermediate Similarity NPC469692
0.7889 Intermediate Similarity NPC469645
0.7821 Intermediate Similarity NPC475982
0.7816 Intermediate Similarity NPC469910
0.7802 Intermediate Similarity NPC121825
0.7753 Intermediate Similarity NPC130359
0.7753 Intermediate Similarity NPC14901
0.7753 Intermediate Similarity NPC79027
0.7727 Intermediate Similarity NPC178215
0.7722 Intermediate Similarity NPC202011
0.7701 Intermediate Similarity NPC103284
0.7701 Intermediate Similarity NPC1083
0.7701 Intermediate Similarity NPC66346
0.7701 Intermediate Similarity NPC82795
0.7701 Intermediate Similarity NPC473669
0.7701 Intermediate Similarity NPC286338
0.7701 Intermediate Similarity NPC473478
0.7701 Intermediate Similarity NPC283085
0.7701 Intermediate Similarity NPC107986
0.7701 Intermediate Similarity NPC231009
0.7701 Intermediate Similarity NPC132496
0.7701 Intermediate Similarity NPC223871
0.7701 Intermediate Similarity NPC473651
0.7701 Intermediate Similarity NPC470755
0.7701 Intermediate Similarity NPC110710
0.7683 Intermediate Similarity NPC68819
0.7667 Intermediate Similarity NPC474232
0.7654 Intermediate Similarity NPC476590
0.7654 Intermediate Similarity NPC114727
0.7647 Intermediate Similarity NPC297440
0.764 Intermediate Similarity NPC21208
0.764 Intermediate Similarity NPC280621
0.764 Intermediate Similarity NPC476803
0.764 Intermediate Similarity NPC40376
0.764 Intermediate Similarity NPC287089
0.764 Intermediate Similarity NPC48338
0.764 Intermediate Similarity NPC20339
0.764 Intermediate Similarity NPC233551
0.7625 Intermediate Similarity NPC186531
0.7614 Intermediate Similarity NPC134885
0.7614 Intermediate Similarity NPC62118
0.7614 Intermediate Similarity NPC231096
0.7614 Intermediate Similarity NPC134807
0.7614 Intermediate Similarity NPC219498
0.7614 Intermediate Similarity NPC112685
0.7614 Intermediate Similarity NPC134865
0.7614 Intermediate Similarity NPC142117
0.7614 Intermediate Similarity NPC475581
0.7614 Intermediate Similarity NPC308412
0.7614 Intermediate Similarity NPC171174
0.7614 Intermediate Similarity NPC114694
0.7614 Intermediate Similarity NPC473687
0.7614 Intermediate Similarity NPC240695
0.7614 Intermediate Similarity NPC232555
0.7614 Intermediate Similarity NPC279267
0.7614 Intermediate Similarity NPC69082
0.7614 Intermediate Similarity NPC103523
0.7614 Intermediate Similarity NPC210218
0.7614 Intermediate Similarity NPC204686
0.7614 Intermediate Similarity NPC107717
0.759 Intermediate Similarity NPC116177
0.759 Intermediate Similarity NPC7563
0.759 Intermediate Similarity NPC320630
0.7586 Intermediate Similarity NPC163093
0.7586 Intermediate Similarity NPC158756
0.7561 Intermediate Similarity NPC478194
0.7561 Intermediate Similarity NPC478193
0.7561 Intermediate Similarity NPC478191
0.7561 Intermediate Similarity NPC478195
0.7561 Intermediate Similarity NPC478196
0.7561 Intermediate Similarity NPC260396
0.7561 Intermediate Similarity NPC478192
0.7558 Intermediate Similarity NPC475159
0.7558 Intermediate Similarity NPC473780
0.7558 Intermediate Similarity NPC180363
0.7558 Intermediate Similarity NPC473712
0.7558 Intermediate Similarity NPC473529
0.7558 Intermediate Similarity NPC11332
0.7558 Intermediate Similarity NPC131002
0.7558 Intermediate Similarity NPC65930
0.7558 Intermediate Similarity NPC329829
0.7558 Intermediate Similarity NPC94875
0.7558 Intermediate Similarity NPC73310
0.7558 Intermediate Similarity NPC145914
0.7556 Intermediate Similarity NPC139418
0.7529 Intermediate Similarity NPC47653
0.75 Intermediate Similarity NPC21469
0.75 Intermediate Similarity NPC288240
0.75 Intermediate Similarity NPC295204
0.75 Intermediate Similarity NPC273579
0.75 Intermediate Similarity NPC93763
0.75 Intermediate Similarity NPC477014
0.75 Intermediate Similarity NPC108816
0.75 Intermediate Similarity NPC120398
0.75 Intermediate Similarity NPC477013
0.75 Intermediate Similarity NPC162205
0.75 Intermediate Similarity NPC182383
0.75 Intermediate Similarity NPC471567
0.7473 Intermediate Similarity NPC473904
0.7473 Intermediate Similarity NPC239517
0.7471 Intermediate Similarity NPC40746
0.7471 Intermediate Similarity NPC161045
0.7471 Intermediate Similarity NPC116543
0.7471 Intermediate Similarity NPC144415
0.7471 Intermediate Similarity NPC253801
0.7471 Intermediate Similarity NPC169575
0.7468 Intermediate Similarity NPC470256
0.7447 Intermediate Similarity NPC477921
0.7444 Intermediate Similarity NPC61257
0.7444 Intermediate Similarity NPC133730
0.7444 Intermediate Similarity NPC151403
0.7444 Intermediate Similarity NPC287164
0.7444 Intermediate Similarity NPC171135
0.7444 Intermediate Similarity NPC234077
0.7444 Intermediate Similarity NPC81045
0.7444 Intermediate Similarity NPC476805
0.7444 Intermediate Similarity NPC169511
0.7444 Intermediate Similarity NPC172821
0.7444 Intermediate Similarity NPC261952
0.7444 Intermediate Similarity NPC320569
0.7444 Intermediate Similarity NPC242364
0.7444 Intermediate Similarity NPC191929
0.7444 Intermediate Similarity NPC475819
0.7444 Intermediate Similarity NPC39754
0.7444 Intermediate Similarity NPC274446
0.7444 Intermediate Similarity NPC100454
0.7416 Intermediate Similarity NPC47937
0.7416 Intermediate Similarity NPC469483
0.7416 Intermediate Similarity NPC475461
0.7416 Intermediate Similarity NPC305475
0.7416 Intermediate Similarity NPC477015
0.7391 Intermediate Similarity NPC473321
0.7386 Intermediate Similarity NPC41856
0.7386 Intermediate Similarity NPC156804
0.7363 Intermediate Similarity NPC280612
0.7363 Intermediate Similarity NPC91067
0.7363 Intermediate Similarity NPC473504
0.7363 Intermediate Similarity NPC93794
0.7363 Intermediate Similarity NPC20621
0.7363 Intermediate Similarity NPC81778
0.7363 Intermediate Similarity NPC42598
0.7363 Intermediate Similarity NPC477011
0.7363 Intermediate Similarity NPC40066
0.7363 Intermediate Similarity NPC318963
0.7342 Intermediate Similarity NPC194871
0.7342 Intermediate Similarity NPC225272
0.734 Intermediate Similarity NPC471142
0.734 Intermediate Similarity NPC477922
0.7326 Intermediate Similarity NPC162741
0.7326 Intermediate Similarity NPC91332
0.7326 Intermediate Similarity NPC121374
0.732 Intermediate Similarity NPC133907
0.732 Intermediate Similarity NPC185141
0.732 Intermediate Similarity NPC110443
0.732 Intermediate Similarity NPC46998
0.732 Intermediate Similarity NPC128733
0.7317 Intermediate Similarity NPC144419
0.7312 Intermediate Similarity NPC475912
0.7312 Intermediate Similarity NPC11456
0.7308 Intermediate Similarity NPC19769
0.7308 Intermediate Similarity NPC470123
0.7308 Intermediate Similarity NPC282760
0.7303 Intermediate Similarity NPC473156
0.7303 Intermediate Similarity NPC329615
0.7303 Intermediate Similarity NPC77871
0.7303 Intermediate Similarity NPC470400
0.7303 Intermediate Similarity NPC39279
0.7303 Intermediate Similarity NPC235809
0.7303 Intermediate Similarity NPC202055
0.7303 Intermediate Similarity NPC473671
0.7303 Intermediate Similarity NPC329838
0.7303 Intermediate Similarity NPC322529
0.7303 Intermediate Similarity NPC475268
0.7303 Intermediate Similarity NPC477018
0.7303 Intermediate Similarity NPC11804
0.7303 Intermediate Similarity NPC319036

  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 NPC150502 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
0.7292 Intermediate Similarity NPD4225 Approved
0.6737 Remote Similarity NPD6698 Approved
0.6737 Remote Similarity NPD46 Approved
0.6737 Remote Similarity NPD5785 Approved
0.6635 Remote Similarity NPD7899 Clinical (unspecified phase)
0.6633 Remote Similarity NPD1698 Clinical (unspecified phase)
0.6604 Remote Similarity NPD6371 Approved
0.6562 Remote Similarity NPD7838 Discovery
0.6559 Remote Similarity NPD5363 Approved
0.6559 Remote Similarity NPD6082 Clinical (unspecified phase)
0.6495 Remote Similarity NPD7983 Approved
0.6452 Remote Similarity NPD6400 Clinical (unspecified phase)
0.6413 Remote Similarity NPD5209 Approved
0.6383 Remote Similarity NPD1733 Clinical (unspecified phase)
0.6375 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6374 Remote Similarity NPD5790 Clinical (unspecified phase)
0.6374 Remote Similarity NPD4252 Approved
0.6344 Remote Similarity NPD5332 Approved
0.6344 Remote Similarity NPD5331 Approved
0.6344 Remote Similarity NPD7154 Phase 3
0.6275 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6265 Remote Similarity NPD2685 Clinical (unspecified phase)
0.625 Remote Similarity NPD7115 Discovery
0.6237 Remote Similarity NPD4270 Approved
0.6237 Remote Similarity NPD4269 Approved
0.6222 Remote Similarity NPD4756 Discovery
0.6154 Remote Similarity NPD4271 Approved
0.6154 Remote Similarity NPD4268 Approved
0.6146 Remote Similarity NPD4249 Approved
0.6146 Remote Similarity NPD5786 Approved
0.6145 Remote Similarity NPD3197 Phase 1
0.6125 Remote Similarity NPD6109 Phase 1
0.6082 Remote Similarity NPD4250 Approved
0.6082 Remote Similarity NPD4251 Approved
0.6053 Remote Similarity NPD6927 Phase 3
0.6022 Remote Similarity NPD4819 Approved
0.6022 Remote Similarity NPD4821 Approved
0.6022 Remote Similarity NPD4822 Approved
0.6022 Remote Similarity NPD4820 Approved
0.6 Remote Similarity NPD5344 Discontinued
0.6 Remote Similarity NPD5362 Discontinued
0.6 Remote Similarity NPD7637 Suspended
0.5963 Remote Similarity NPD6686 Approved
0.596 Remote Similarity NPD5370 Suspended
0.5957 Remote Similarity NPD5369 Approved
0.5946 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5941 Remote Similarity NPD5778 Approved
0.5941 Remote Similarity NPD5779 Approved
0.593 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5926 Remote Similarity NPD9119 Approved
0.5926 Remote Similarity NPD585 Clinical (unspecified phase)
0.5926 Remote Similarity NPD69 Approved
0.5876 Remote Similarity NPD1694 Approved
0.5842 Remote Similarity NPD4810 Clinical (unspecified phase)
0.5833 Remote Similarity NPD6110 Phase 1
0.5806 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5802 Remote Similarity NPD9118 Approved
0.58 Remote Similarity NPD1695 Approved
0.5789 Remote Similarity NPD4790 Discontinued
0.5769 Remote Similarity NPD7839 Suspended
0.5763 Remote Similarity NPD8513 Phase 3
0.5763 Remote Similarity NPD8515 Approved
0.5763 Remote Similarity NPD8516 Approved
0.5763 Remote Similarity NPD8517 Approved
0.5755 Remote Similarity NPD7639 Approved
0.5755 Remote Similarity NPD7640 Approved
0.575 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5729 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5664 Remote Similarity NPD2204 Approved
0.566 Remote Similarity NPD7638 Approved
0.5644 Remote Similarity NPD6101 Approved
0.5644 Remote Similarity NPD5764 Clinical (unspecified phase)
0.5619 Remote Similarity NPD4792 Clinical (unspecified phase)
0.5607 Remote Similarity NPD6648 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