Structure

Physi-Chem Properties

Molecular Weight:  417.91
Volume:  280.113
LogP:  5.281
LogD:  3.968
LogS:  -4.969
# Rotatable Bonds:  9
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.386
Synthetic Accessibility Score:  3.499
Fsp3:  0.833
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:  -4.488
MDCK Permeability:  1.3867443158233073e-05
Pgp-inhibitor:  0.447
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.052
20% Bioavailability (F20%):  0.077
30% Bioavailability (F30%):  0.941

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.599
Plasma Protein Binding (PPB):  98.21715545654297%
Volume Distribution (VD):  1.464
Pgp-substrate:  2.9929847717285156%

ADMET: Metabolism

CYP1A2-inhibitor:  0.9
CYP1A2-substrate:  0.735
CYP2C19-inhibitor:  0.962
CYP2C19-substrate:  0.697
CYP2C9-inhibitor:  0.949
CYP2C9-substrate:  0.971
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.211
CYP3A4-inhibitor:  0.803
CYP3A4-substrate:  0.518

ADMET: Excretion

Clearance (CL):  1.34
Half-life (T1/2):  0.245

ADMET: Toxicity

hERG Blockers:  0.049
Human Hepatotoxicity (H-HT):  0.73
Drug-inuced Liver Injury (DILI):  0.451
AMES Toxicity:  0.1
Rat Oral Acute Toxicity:  0.304
Maximum Recommended Daily Dose:  0.048
Skin Sensitization:  0.922
Carcinogencity:  0.584
Eye Corrosion:  0.398
Eye Irritation:  0.873
Respiratory Toxicity:  0.956

Download Data

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

  Natural Product: NPC475071

Natural Product ID:  NPC475071
Common Name*:   Sid527763
IUPAC Name:   (Z)-1,1,3-tribromododec-3-en-2-ol
Synonyms:  
Standard InCHIKey:  OXAKHAUHUJIBEU-KTKRTIGZSA-N
Standard InCHI:  InChI=1S/C12H21Br3O/c1-2-3-4-5-6-7-8-9-10(13)11(16)12(14)15/h9,11-12,16H,2-8H2,1H3/b10-9-
SMILES:  CCCCCCCCC=C(C(C(Br)Br)O)Br
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL495663
PubChem CID:   5470528
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000267] Organohalogen compounds
      • [CHEMONTID:0002528] Halohydrins
        • [CHEMONTID:0002607] Bromohydrins

*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
NPO14524 Delisea pulchra Species Bonnemaisoniaceae Eukaryota n.a. n.a. n.a. PMID[16933872]
NPO14524 Delisea pulchra Species Bonnemaisoniaceae 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
NPT367 Cell Line MDA-N Homo sapiens GI50 n.a. 21777.1 nM PMID[487054]
NPT368 Cell Line SN12C Homo sapiens GI50 n.a. 17298.16 nM PMID[487054]
NPT369 Cell Line ACHN Homo sapiens GI50 n.a. 22335.72 nM PMID[487054]
NPT370 Cell Line NCI-H23 Homo sapiens GI50 n.a. 22080.05 nM PMID[487054]
NPT371 Cell Line UO-31 Homo sapiens GI50 n.a. 19364.22 nM PMID[487054]
NPT372 Cell Line HOP-92 Homo sapiens GI50 n.a. 20892.96 nM PMID[487054]
NPT90 Cell Line DU-145 Homo sapiens GI50 n.a. 38636.7 nM PMID[487054]
NPT373 Cell Line SK-MEL-5 Homo sapiens GI50 n.a. 17906.06 nM PMID[487054]
NPT375 Cell Line Malme-3M Homo sapiens GI50 n.a. 21134.89 nM PMID[487054]
NPT111 Cell Line K562 Homo sapiens GI50 n.a. 69662.65 nM PMID[487054]
NPT376 Cell Line A498 Homo sapiens GI50 n.a. 31045.6 nM PMID[487054]
NPT377 Cell Line OVCAR-3 Homo sapiens GI50 n.a. 17378.01 nM PMID[487054]
NPT112 Cell Line MOLT-4 Homo sapiens GI50 n.a. 100000.0 nM PMID[487054]
NPT379 Cell Line HOP-62 Homo sapiens GI50 n.a. 19633.6 nM PMID[487054]
NPT378 Cell Line NCI/ADR-RES Homo sapiens GI50 n.a. 26242.19 nM PMID[487054]
NPT381 Cell Line OVCAR-8 Homo sapiens GI50 n.a. 23442.29 nM PMID[487054]
NPT380 Cell Line U-251 Homo sapiens GI50 n.a. 29991.63 nM PMID[487054]
NPT382 Cell Line OVCAR-5 Homo sapiens GI50 n.a. 19275.25 nM PMID[487054]
NPT82 Cell Line MDA-MB-231 Homo sapiens GI50 n.a. 36812.9 nM PMID[487054]
NPT383 Cell Line SNB-19 Homo sapiens GI50 n.a. 31841.98 nM PMID[487054]
NPT385 Cell Line SR Homo sapiens GI50 n.a. 40831.94 nM PMID[487054]
NPT384 Cell Line TK-10 Homo sapiens GI50 n.a. 39445.73 nM PMID[487054]
NPT323 Cell Line SW-620 Homo sapiens GI50 n.a. 16255.49 nM PMID[487054]
NPT455 Cell Line NCI-H522 Homo sapiens GI50 n.a. 19142.56 nM PMID[487054]
NPT386 Cell Line KM12 Homo sapiens GI50 n.a. 19054.61 nM PMID[487054]
NPT387 Cell Line M14 Homo sapiens GI50 n.a. 22698.65 nM PMID[487054]
NPT388 Cell Line NCI-H322M Homo sapiens GI50 n.a. 31045.6 nM PMID[487054]
NPT389 Cell Line RPMI-8226 Homo sapiens GI50 n.a. 42657.95 nM PMID[487054]
NPT456 Cell Line OVCAR-4 Homo sapiens GI50 n.a. 20606.3 nM PMID[487054]
NPT390 Cell Line LOX IMVI Homo sapiens GI50 n.a. 19860.95 nM PMID[487054]
NPT457 Cell Line BT-549 Homo sapiens GI50 n.a. 22438.82 nM PMID[487054]
NPT147 Cell Line SK-MEL-2 Homo sapiens GI50 n.a. 24831.33 nM PMID[487054]
NPT391 Cell Line HCC 2998 Homo sapiens GI50 n.a. 18836.49 nM PMID[487054]
NPT81 Cell Line A549 Homo sapiens GI50 n.a. 31405.09 nM PMID[487054]
NPT392 Cell Line SNB-75 Homo sapiens GI50 n.a. 35974.93 nM PMID[487054]
NPT148 Cell Line HCT-15 Homo sapiens GI50 n.a. 20558.91 nM PMID[487054]
NPT393 Cell Line HCT-116 Homo sapiens GI50 n.a. 27164.39 nM PMID[487054]
NPT395 Cell Line SF-268 Homo sapiens GI50 n.a. 23227.37 nM PMID[487054]
NPT394 Cell Line EKVX Homo sapiens GI50 n.a. 28248.8 nM PMID[487054]
NPT306 Cell Line PC-3 Homo sapiens GI50 n.a. 38106.58 nM PMID[487054]
NPT83 Cell Line MCF7 Homo sapiens GI50 n.a. 25468.3 nM PMID[487054]
NPT146 Cell Line SK-OV-3 Homo sapiens GI50 n.a. 26607.25 nM PMID[487054]
NPT396 Cell Line T47D Homo sapiens GI50 n.a. 30974.19 nM PMID[487054]
NPT397 Cell Line NCI-H460 Homo sapiens GI50 n.a. 30408.85 nM PMID[487054]
NPT398 Cell Line UACC-62 Homo sapiens GI50 n.a. 19319.68 nM PMID[487054]
NPT308 Cell Line CAKI-1 Homo sapiens GI50 n.a. 19498.45 nM PMID[487054]
NPT400 Cell Line MDA-MB-435 Homo sapiens GI50 n.a. 21478.3 nM PMID[487054]
NPT399 Cell Line SF-295 Homo sapiens GI50 n.a. 17988.71 nM PMID[487054]
NPT458 Cell Line IGROV-1 Homo sapiens GI50 n.a. 24660.39 nM PMID[487054]
NPT402 Cell Line Hs-578T Homo sapiens GI50 n.a. 22750.97 nM PMID[487054]
NPT401 Cell Line 786-0 Homo sapiens GI50 n.a. 18492.69 nM PMID[487054]
NPT403 Cell Line UACC-257 Homo sapiens GI50 n.a. 27989.81 nM PMID[487054]
NPT404 Cell Line CCRF-CEM Homo sapiens GI50 n.a. 16069.41 nM PMID[487054]
NPT170 Cell Line SK-MEL-28 Homo sapiens GI50 n.a. 29241.52 nM PMID[487054]
NPT406 Cell Line RXF 393 Homo sapiens GI50 n.a. 19275.25 nM PMID[487054]
NPT407 Cell Line COLO 205 Homo sapiens GI50 n.a. 18923.44 nM PMID[487054]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 8.0 mm PMID[487053]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 5.0 mm PMID[487053]
NPT2 Others Unspecified IC50 >= 200000.0 nM PMID[487053]

☑ 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 NPC475071 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
0.75 Intermediate Similarity NPC248884
0.75 Intermediate Similarity NPC85079
0.75 Intermediate Similarity NPC31194
0.7451 Intermediate Similarity NPC55063
0.7451 Intermediate Similarity NPC19834
0.7447 Intermediate Similarity NPC15934
0.7358 Intermediate Similarity NPC474642
0.7358 Intermediate Similarity NPC249670
0.7358 Intermediate Similarity NPC473913
0.7358 Intermediate Similarity NPC72699
0.7255 Intermediate Similarity NPC269074
0.7222 Intermediate Similarity NPC473672
0.7222 Intermediate Similarity NPC151782
0.7222 Intermediate Similarity NPC474495
0.717 Intermediate Similarity NPC471280
0.717 Intermediate Similarity NPC125122
0.717 Intermediate Similarity NPC471275
0.717 Intermediate Similarity NPC471276
0.717 Intermediate Similarity NPC153538
0.7115 Intermediate Similarity NPC124183
0.7115 Intermediate Similarity NPC35141
0.7083 Intermediate Similarity NPC182840
0.7083 Intermediate Similarity NPC103213
0.7083 Intermediate Similarity NPC255042
0.7083 Intermediate Similarity NPC29091
0.7059 Intermediate Similarity NPC101616
0.7037 Intermediate Similarity NPC471281
0.7037 Intermediate Similarity NPC477727
0.7037 Intermediate Similarity NPC199286
0.7 Intermediate Similarity NPC304151
0.6909 Remote Similarity NPC55383
0.6909 Remote Similarity NPC256656
0.6909 Remote Similarity NPC197272
0.6909 Remote Similarity NPC165447
0.6909 Remote Similarity NPC294278
0.6909 Remote Similarity NPC76198
0.6909 Remote Similarity NPC477723
0.6909 Remote Similarity NPC9273
0.6909 Remote Similarity NPC89824
0.6909 Remote Similarity NPC224148
0.6909 Remote Similarity NPC71053
0.6909 Remote Similarity NPC59408
0.6909 Remote Similarity NPC329608
0.6909 Remote Similarity NPC93639
0.6909 Remote Similarity NPC471959
0.6909 Remote Similarity NPC475477
0.6909 Remote Similarity NPC170776
0.6842 Remote Similarity NPC49059
0.6842 Remote Similarity NPC256209
0.68 Remote Similarity NPC269823
0.6792 Remote Similarity NPC180575
0.6786 Remote Similarity NPC142092
0.6727 Remote Similarity NPC26960
0.6727 Remote Similarity NPC473768
0.6727 Remote Similarity NPC182102
0.6724 Remote Similarity NPC474644
0.6667 Remote Similarity NPC46248
0.6667 Remote Similarity NPC474496
0.6667 Remote Similarity NPC213538
0.6667 Remote Similarity NPC206906
0.6667 Remote Similarity NPC249801
0.6667 Remote Similarity NPC256766
0.661 Remote Similarity NPC473865
0.661 Remote Similarity NPC474643
0.6607 Remote Similarity NPC244038
0.6596 Remote Similarity NPC58957
0.6552 Remote Similarity NPC110732
0.6552 Remote Similarity NPC48058
0.6552 Remote Similarity NPC473532
0.6545 Remote Similarity NPC477789
0.6545 Remote Similarity NPC475153
0.6538 Remote Similarity NPC116934
0.6538 Remote Similarity NPC252978
0.65 Remote Similarity NPC193975
0.6491 Remote Similarity NPC35756
0.6452 Remote Similarity NPC477430
0.6441 Remote Similarity NPC146551
0.6441 Remote Similarity NPC473725
0.6441 Remote Similarity NPC232247
0.6441 Remote Similarity NPC477725
0.6441 Remote Similarity NPC474513
0.6441 Remote Similarity NPC473896
0.6441 Remote Similarity NPC470963
0.6441 Remote Similarity NPC317899
0.6441 Remote Similarity NPC473910
0.6441 Remote Similarity NPC475353
0.6441 Remote Similarity NPC329686
0.6441 Remote Similarity NPC251666
0.6441 Remote Similarity NPC471239
0.6441 Remote Similarity NPC473721
0.6441 Remote Similarity NPC477726
0.6441 Remote Similarity NPC473735
0.6429 Remote Similarity NPC291437
0.6429 Remote Similarity NPC328784
0.6415 Remote Similarity NPC108195
0.6415 Remote Similarity NPC138935
0.6383 Remote Similarity NPC250734
0.6379 Remote Similarity NPC217188
0.6379 Remote Similarity NPC61177
0.6346 Remote Similarity NPC149668
0.6333 Remote Similarity NPC311648
0.6333 Remote Similarity NPC470967
0.6333 Remote Similarity NPC475384
0.6333 Remote Similarity NPC470969
0.6333 Remote Similarity NPC471960
0.6333 Remote Similarity NPC473847
0.6333 Remote Similarity NPC161838
0.6333 Remote Similarity NPC470968
0.6333 Remote Similarity NPC48891
0.6333 Remote Similarity NPC470964
0.6333 Remote Similarity NPC470966
0.6333 Remote Similarity NPC477661
0.6316 Remote Similarity NPC129263
0.6296 Remote Similarity NPC160628
0.6296 Remote Similarity NPC140501
0.6296 Remote Similarity NPC76976
0.629 Remote Similarity NPC122239
0.6271 Remote Similarity NPC189677
0.6269 Remote Similarity NPC477431
0.625 Remote Similarity NPC267110
0.625 Remote Similarity NPC302310
0.623 Remote Similarity NPC212730
0.623 Remote Similarity NPC470970
0.623 Remote Similarity NPC265551
0.623 Remote Similarity NPC48968
0.623 Remote Similarity NPC594
0.623 Remote Similarity NPC44542
0.62 Remote Similarity NPC40434
0.62 Remote Similarity NPC34873
0.619 Remote Similarity NPC471081
0.619 Remote Similarity NPC471278
0.6176 Remote Similarity NPC316572
0.6167 Remote Similarity NPC152668
0.6167 Remote Similarity NPC227135
0.6167 Remote Similarity NPC298299
0.6154 Remote Similarity NPC271000
0.614 Remote Similarity NPC474460
0.614 Remote Similarity NPC288381
0.614 Remote Similarity NPC20934
0.6133 Remote Similarity NPC311891
0.6129 Remote Similarity NPC181872
0.6129 Remote Similarity NPC226848
0.6129 Remote Similarity NPC155025
0.6122 Remote Similarity NPC79544
0.6102 Remote Similarity NPC475723
0.6102 Remote Similarity NPC34577
0.6094 Remote Similarity NPC271282
0.6094 Remote Similarity NPC66460
0.6094 Remote Similarity NPC325929
0.6066 Remote Similarity NPC55412
0.6066 Remote Similarity NPC472808
0.6066 Remote Similarity NPC324224
0.6066 Remote Similarity NPC249645
0.6042 Remote Similarity NPC81989
0.6034 Remote Similarity NPC29234
0.6032 Remote Similarity NPC475931
0.6032 Remote Similarity NPC473652
0.6 Remote Similarity NPC473508
0.6 Remote Similarity NPC113024
0.6 Remote Similarity NPC276825
0.6 Remote Similarity NPC29697
0.6 Remote Similarity NPC55068
0.6 Remote Similarity NPC474155
0.6 Remote Similarity NPC216416
0.6 Remote Similarity NPC473759
0.5968 Remote Similarity NPC11130
0.5962 Remote Similarity NPC329762
0.5962 Remote Similarity NPC27444
0.5962 Remote Similarity NPC103236
0.5938 Remote Similarity NPC99487
0.5938 Remote Similarity NPC240506
0.5938 Remote Similarity NPC327112
0.5909 Remote Similarity NPC470320
0.5909 Remote Similarity NPC300593
0.5909 Remote Similarity NPC471460
0.5902 Remote Similarity NPC130209
0.5902 Remote Similarity NPC148216
0.5902 Remote Similarity NPC148163
0.5893 Remote Similarity NPC157096
0.5857 Remote Similarity NPC477423
0.5846 Remote Similarity NPC168407
0.5846 Remote Similarity NPC207007
0.5846 Remote Similarity NPC68679
0.5846 Remote Similarity NPC475984
0.5846 Remote Similarity NPC113293
0.5846 Remote Similarity NPC225342
0.5846 Remote Similarity NPC321867
0.5833 Remote Similarity NPC187361
0.5833 Remote Similarity NPC26102
0.5833 Remote Similarity NPC477724
0.5821 Remote Similarity NPC245947
0.5821 Remote Similarity NPC308844
0.5821 Remote Similarity NPC255863
0.5821 Remote Similarity NPC136164
0.5821 Remote Similarity NPC19569
0.5818 Remote Similarity NPC474413
0.5818 Remote Similarity NPC473539
0.58 Remote Similarity NPC213767
0.5797 Remote Similarity NPC471472
0.5797 Remote Similarity NPC473294

  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 NPC475071 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
0.6296 Remote Similarity NPD4265 Approved
0.6066 Remote Similarity NPD4219 Approved
0.6 Remote Similarity NPD3210 Clinical (unspecified phase)
0.5938 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5902 Remote Similarity NPD342 Phase 1
0.5846 Remote Similarity NPD368 Approved
0.5625 Remote Similarity NPD585 Clinical (unspecified phase)

  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