ITCMDBv1
IngredientID 1026

2,5-dihydroxymethyl-3,4-dihydroxypyrrolidine

C6H13NO4

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Herb: 4Ingredient: 1Target: 12Links: 22
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Record Fields

Scalar fields from the final ingredient record.

Ingredient Id
1026
Core Entity Id
4336
Source Entity Count
1
Preferred Name
2,5-dihydroxymethyl-3,4-dihydroxypyrrolidine
Name En
Pubchem Id
124702
Smiles Canonical
C(C1C(C(C(N1)CO)O)O)O
Molecular Formula
C6H13NO4
Molecular Weight
163.1730
Inchikey
PFYHYHZGDNWFIF-KVTDHHQDSA-N
Inchi
InChI=1S/C6H13NO4/c8-1-3-5(10)6(11)4(2-9)7-3/h3-11H,1-2H2/t3-,4-,5-,6-/m1/s1
Isomeric Smiles
C([C@@H]1[C@H]([C@@H]([C@H](N1)CO)O)O)O
Cas Id
Ob Score
Mol Logp
-2.9668
Num H Donors
5
Num H Acceptors
5
Num Rotatable Bonds
2
Drug Likeness
0.3000
Polar Surface Area
92.9500
Molecular Volume
129.9900
Alogp
-2.4400

Names

Preferred names, aliases, and source labels retained in the final schema.

Name
2,5-Dihydroxymethyl-3,4-Dihydroxypyrrolidine
Role
preferred
Source
SymMap_v2
Preferred
Yes
Name
2,5-Dihydroxymethyl-3,4-dihydroxypyrrolidine
Role
preferred
Source
ETCM_v2
Preferred
Yes
Name
2,5-dihydroxymethyl-3,4-dihydroxypyrrolidine
Role
preferred
Source
HERB_v2
Preferred
Yes
Name
2,5-dihydroxymethyl-3,4-dihydroxypyrrolidine
Role
preferred
Source
itcmdb_public
Preferred
Yes
Name
2,5-dihydroxymethyl-3,4-dihydroxypyrrolidine
Role
preferred
Source
TCMBank
Preferred
Yes
Name
(2R,3R,4R,5R)-2,5-Bis-hydroxymethyl-pyrrolidine-3,4-diol
Role
alias
Source
TCMBank
Preferred
No
Name
(2R,3R,4R,5R)-2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol
Role
alias
Source
HERB_v2
Preferred
No
Name
(2R,3R,4R,5R)-2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol
Role
alias
Source
itcmdb_public
Preferred
No
Name
2(r),5(r)-bis(hydroxymethyl)-3(r),4(r)-dihydroxypyrrolidine
Role
alias
Source
TCMBank
Preferred
No
Name
2,5-Anhydro-2,5-imino-D-mannitol
Role
alias
Source
HERB_v2
Preferred
No
Name
2,5-Anhydro-2,5-imino-D-mannitol
Role
alias
Source
itcmdb_public
Preferred
No
Name
2,5-Anhydro-2,5-imino-D-mannitol
Role
alias
Source
TCMBank
Preferred
No
Name
2,5-Dideoxy-2,5-imino-D-mannitol
Role
alias
Source
itcmdb_public
Preferred
No
Name
2,5-Dideoxy-2,5-imino-D-mannitol
Role
alias
Source
TCMBank
Preferred
No
Name
2,5-Dideoxy-2,5-imino-D-mannitol
Role
alias
Source
HERB_v2
Preferred
No
Name
2,5-Dihydroxymethyl-3,4-dihydroxypyrrolidine
Role
alias
Source
TCMBank
Preferred
No
Name
2,5-Pyrrolidinedimethanol, 3,4-dihydroxy-, (2R,3R,4R,5R)-
Role
alias
Source
TCMBank
Preferred
No
Name
2,5-bis(hydroxymethyl)-3,4-dihydroxypyrrolidine
Role
alias
Source
itcmdb_public
Preferred
No
Name
2,5-bis(hydroxymethyl)-3,4-dihydroxypyrrolidine
Role
alias
Source
TCMBank
Preferred
No
Name
2,5-bis(hydroxymethyl)-3,4-dihydroxypyrrolidine
Role
alias
Source
HERB_v2
Preferred
No
Name
2,5-imino-2,5-dideoxy-d-mannitol
Role
alias
Source
TCMBank
Preferred
No
Name
2R,5R-dihydroxymethyl-3R,4R-dihydroxypyrrolidine
Role
alias
Source
TCMBank
Preferred
No
Name
59920-31-9
Role
alias
Source
HERB_v2
Preferred
No
Name
59920-31-9
Role
alias
Source
TCMBank
Preferred
No
Name
59920-31-9
Role
alias
Source
itcmdb_public
Preferred
No
Name
9D7F3C44-69AD-44CB-89DE-8A2E1A4AE7D1
Role
alias
Source
TCMBank
Preferred
No
Name
AC1L3YWM
Role
alias
Source
TCMBank
Preferred
No
Name
AC1Q59GS
Role
alias
Source
TCMBank
Preferred
No
Name
AK307911
Role
alias
Source
TCMBank
Preferred
No
Name
AKOS006280967
Role
alias
Source
TCMBank
Preferred
No
Name
Ambap59920-31-9
Role
alias
Source
TCMBank
Preferred
No
Name
BDBM50031481
Role
alias
Source
TCMBank
Preferred
No
Name
BG00904828
Role
alias
Source
TCMBank
Preferred
No
Name
BG01501291
Role
alias
Source
TCMBank
Preferred
No
Name
C10143
Role
alias
Source
TCMBank
Preferred
No
Name
CHEBI:4289
Role
alias
Source
HERB_v2
Preferred
No
Name
CHEBI:4289
Role
alias
Source
TCMBank
Preferred
No
Name
CHEBI:4289
Role
alias
Source
itcmdb_public
Preferred
No
Name
CHEMBL312653
Role
alias
Source
HERB_v2
Preferred
No
Name
CHEMBL312653
Role
alias
Source
TCMBank
Preferred
No
Name
CHEMBL312653
Role
alias
Source
itcmdb_public
Preferred
No
Name
D-Mannitol, 2,5-dideoxy-2,5-imino-, (6R-(6alpha,7alpha,7(R*)))-
Role
alias
Source
TCMBank
Preferred
No
Name
D0R5HV
Role
alias
Source
TCMBank
Preferred
No
Name
DQQ
Role
alias
Source
TCMBank
Preferred
No
Name
FT-0610339
Role
alias
Source
TCMBank
Preferred
No
Name
FT-0662198
Role
alias
Source
TCMBank
Preferred
No
Name
NSC 624987
Role
alias
Source
TCMBank
Preferred
No
Name
NSC613239
Role
alias
Source
HERB_v2
Preferred
No
Name
NSC613239
Role
alias
Source
TCMBank
Preferred
No
Name
NSC613239
Role
alias
Source
itcmdb_public
Preferred
No
Name
NSC624987
Role
alias
Source
HERB_v2
Preferred
No
Name
NSC624987
Role
alias
Source
itcmdb_public
Preferred
No
Name
SCHEMBL466574
Role
alias
Source
TCMBank
Preferred
No
Name
W-203234
Role
alias
Source
TCMBank
Preferred
No
Name
ZINC1492230
Role
alias
Source
TCMBank
Preferred
No
Name
毛鱼藤
Role
TCM_name
Source
TCMBank
Preferred
No
Name
MAO YU TENG
Role
TCM_name2
Source
TCMBank
Preferred
No
Name
Tubaroot Jewelvine
Role
TCM_name_en
Source
TCMBank
Preferred
No

Aliases

Additional names normalized into the restored final schema.

(2R,3R,4R,5R)-2,5-Bis-hydroxymethyl-pyrrolidine-3,4-diol(2R,3R,4R,5R)-2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol2(r),5(r)-bis(hydroxymethyl)-3(r),4(r)-dihydroxypyrrolidine2,5-Anhydro-2,5-imino-D-mannitol2,5-Dideoxy-2,5-imino-D-mannitol2,5-Pyrrolidinedimethanol, 3,4-dihydroxy-, (2R,3R,4R,5R)-2,5-bis(hydroxymethyl)-3,4-dihydroxypyrrolidine2,5-imino-2,5-dideoxy-d-mannitol2R,5R-dihydroxymethyl-3R,4R-dihydroxypyrrolidine59920-31-99D7F3C44-69AD-44CB-89DE-8A2E1A4AE7D1AC1L3YWMAC1Q59GSAK307911AKOS006280967Ambap59920-31-9BDBM50031481BG00904828BG01501291C10143CHEBI:4289CHEMBL312653D-Mannitol, 2,5-dideoxy-2,5-imino-, (6R-(6alpha,7alpha,7(R*)))-D0R5HVDQQFT-0610339FT-0662198NSC 624987NSC613239NSC624987SCHEMBL466574W-203234ZINC1492230毛鱼藤MAO YU TENGTubaroot Jewelvine

Cross References

Trusted external identifiers retained for this final record.

Herb
HBIN004636
Npass
NPC8087
Tcmid
6027
Sym Map
SMIT15123
Pub Chem
124702
Tcmbank
TCMBANKIN026290TCMBANKIN050804
Etcm Ingredient
2,5-Dihydroxymethyl-3,4-dihydroxypyrrolidine
Itcmdb Generated
ITX-INGREDIENT-519168DCC60BITX-INGREDIENT-54D3A24FA0C4

Attributes

Merged source attributes and domain-specific metadata.

Ic
2.55034
Jx
2.40167
Jy
2.57201
Bic
0.73721
Cic
0.90909
Phi
2.80093
Sic
0.73721
Log D
-3.476
Sc 0
11
Sc 1
11
Sc 2
15
Type
Other ingredients
Alog P
-2.44
Chi 0
8.43072
Chi 1
5.2019
Chi 2
4.29059
In Ch I
InChI=1S/C6H13NO4/c8-1-3-5(10)6(11)4(2-9)7-3/h3-11H,1-2H2/t3-,4-,5-,6-/m1/s1
Mol Wt
163.173
Pmi X
41.8782
Energy
22.05
Sc 3 C
4
Sc 3 P
20
Smiles
C(C1C(C(C(N1)CO)O)O)O
Zagreb
52
Chi 3 C
0.71823
Chi 3 P
3.97073
Chi V 0
6.01246
Chi V 1
3.5427
Chi V 2
2.72598
Kappa 1
9.0909
Kappa 2
3.59999
Kappa 3
1.6
Mol Log P
-2.966799999999998
Sc 3 Ch
0
Version
v1,v2
Alog P Mr
36.574
Chi 3 Ch
0
Dipole X
-0.32345
Dipole Y
0.56071
Dipole Z
0.26508
Iac Mean
1.60098
In Ch Ikey
PFYHYHZGDNWFIF-KVTDHHQDSA-N
Is Chiral
0
Suppress
0
Tcm Name
毛鱼藤
Chi V 3 C
0.40783
Chi V 3 P
1.99596
Es Sum D O
0
Es Sum T N
0
E Adj Equ
97.7664
E Adj Mag
147.207
Hba Count
0
Hbd Count
5
Iac Total
38.4236
Jurs Rasa
0.36199
Jurs Rncg
0.21119
Jurs Rncs
9.09678
Jurs Rpcg
0.22566
Jurs Rpcs
2.39815
Jurs Rpsa
0.638
Jurs Sasa
304.246
Jurs Tasa
110.136
Jurs Tpsa
194.11
Num Atoms
11
Num Bonds
11
Num Rings
1
Shadow Xy
44.2121
Shadow Xz
29.6168
Shadow Yz
21.163
Shadow Nu
2.38072
Tcm Name2
MAO YU TENG
V Adj Equ
82.7686
V Adj Mag
98.1075
Mol2 Path
/TCM_database/2003_3d_all/2432.mol2
Reference
658
Chi V 3 Ch
0
Dipole Mag
0.69949
Es Sum Aa N
0
Es Sum Aa O
0
Es Sum D Nh
0
Es Sum Dd C
0
Es Sum Ds N
0
Es Sum S Oh
35.655
Es Sum Ss O
0
Es Sum T Ch
0
Es Sum Ts C
0
Kappa 1 Am
8.89259
Kappa 2 Am
3.46471
Kappa 3 Am
1.52084
Num Hdonors
5
Num Chains
4
Num Rings3
0
Num Rings4
0
Num Rings5
1
Num Rings6
0
Num Rings7
0
Num Rings8
0
Es Count D O
0
Es Count T N
0
Es Sum Aa Ch
0
Es Sum Aa Nh
0
Es Sum Aaa C
0
Es Sum Aas C
0
Es Sum Aas N
0
Es Sum D Ch2
0
Es Sum Dds N
0
Es Sum Ds Ch
0
Es Sum Dss C
0
Es Sum S Ch3
0
Es Sum S Nh2
0
Es Sum S Nh3
0
Es Sum Ss Nh
2.689
Es Sum Sss N
0
Jurs Dpsa 1
-83.9738
Jurs Dpsa 3
81.7892
Jurs Fnsa 1
0.638
Jurs Fnsa 2
-1.19202
Jurs Fnsa 3
-0.2443
Jurs Fpsa 1
0.36199
Jurs Fpsa 2
0.15886
Jurs Fpsa 3
0.02453
Jurs Pnsa 1
194.11
Jurs Pnsa 2
-362.666
Jurs Pnsa 3
-74.3254
Jurs Ppsa 1
110.136
Jurs Ppsa 3
7.4638
Jurs Wnsa 1
59.057
Jurs Wnsa 2
-110.34
Jurs Wnsa 3
-22.6132
Jurs Wpsa 1
33.5084
Jurs Wpsa 3
2.27083
Num Pi Bonds
0
Tcm Name En
Tubaroot Jewelvine
Admet Psa 2 D
96.072
Es Count Aa N
0
Es Count Aa O
0
Es Count D Nh
0
Es Count Dd C
0
Es Count Ds N
0
Es Count S Oh
4
Es Count Ss O
0
Es Count T Ch
0
Es Count Ts C
0
Es Sum Ss Ch2
-0.483
Es Sum Ss Nh2
0
Es Sum Sss Ch
-3.03
Es Sum Sss Nh
0
Es Sum Ssss C
0
Es Sum Ssss N
0
Nplus O Count
5
Num H Donors
5
Admet Alog P98
-2.44
Admet Ext Ppb
-11.8716
Drug Likeness
0.3
Es Count Aa Ch
0
Es Count Aa Nh
0
Es Count Aaa C
0
Es Count Aas C
0
Es Count Aas N
0
Es Count D Ch2
0
Es Count Dds N
0
Es Count Ds Ch
0
Es Count Dss C
0
Es Count S Ch3
0
Es Count S Nh2
0
Es Count S Nh3
0
Es Count Ss Nh
1
Es Count Sss N
0
Es Sum Sssss P
0
Num Hacceptors
5
Num Fragments
1
Num Hydrogens
13
Num Ring Bonds
5
Organic Count
11
Rad Of Gyration
1.57618
Shadow Xyfrac
0.63492
Shadow Xzfrac
0.74441
Shadow Yzfrac
0.72354
Strain Energy
3.65
Es Count Ss Ch2
2
Es Count Ss Nh2
0
Es Count Sss Ch
4
Es Count Sss Nh
0
Es Count Ssss C
0
Es Count Ssss N
0
Molecular Mass
163.084
Molecular Sasa
316.13
Num Metal Atoms
0
Num Rings9 Plus
0
Shadow Xlength
9.73231
Shadow Ylength
7.15492
Shadow Zlength
4.08797
Admet Bbb Level
4
Isomeric Smiles
C([C@@H]1[C@H]([C@@H]([C@H](N1)CO)O)O)O
Molecular Savol
273.369
Num Atom Classes
6
Num Bridge Bonds
0
Num H Acceptors
5
Num Repeat Units
0
Admet Ext Cyp2 D6
-1.33459
Admet Solubility
2.322
Canonical Smiles
C(C1C(C(C(N1)CO)O)O)O
Herb Alias Names
2,5-Dideoxy-2,5-imino-D-mannitol59920-31-9(2R,3R,4R,5R)-2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol2,5-Anhydro-2,5-imino-D-mannitolCHEBI:4289CHEMBL312653NSC613239NSC6249872,5-bis(hydroxymethyl)-3,4-dihydroxypyrrolidine
Minimized Energy
18.4
Molecular Weight
163.080
Molecular Volume
129.99
Molecular Weight
163.17 g/mol
Molecule Formula
C6H13NO4
Num Macro Chains
0
Molecular Formula
C6H13NO4
Molecular Formula
C6H13NO4
Molecular Formula
C6H13NO4
Num Rotatable Bonds
2
Num Aromatic Bonds
0
Num Aromatic Rings
0
Num Explicit Atoms
11
Num Explicit Bonds
11
Num Negative Atoms
0
Num Positive Atoms
0
Num Macro Residues
0
Num Ring Assemblies
1
Num Rotatable Bonds
2
Molecular Polar Sasa
173.745
Num Bridge Head Atoms
0
Num Chain Assemblies
4
Num Meso Stereo Atoms
4
Molecular Solubility
0.868
Admet Ext Hepatotoxic
-4.15242
Admet Unknown Alog P98
0
Molecular Surface Area
165.19
Num Explicit Hydrogens
0
Num H Donors Lipinski
5
Num Pseudo Stereo Atoms
0
Admet Absorption Level
3
Admet Solubility Level
5
Admet Ext Ppb#Prediction
0
Num H Acceptors Lipinski
5
Molecular Polar Surface Area
92.95
Admet Ext Cyp2 D6#Prediction
0
Molecular Fractional Polar Sasa
0.549
Admet Ext Ppb Applicability#Md
10.6018
Fda Maximum Daily Dose (Fdamdd)
0.055
Admet Ext Hepatotoxic#Prediction
1
Admet Ext Cyp2 D6 Applicability#Md
13.6762
Admet Ext Ppb Applicability#Mdpvalue
0.689029
Molecular Fractional Polar Surface Area
0.562
Admet Ext Hepatotoxic Applicability#Md
6.07469
Admet Ext Cyp2 D6 Applicability#Mdpvalue
5.9e-05
Admet Ext Hepatotoxic Applicability#Mdpvalue
0.999971
Quantitative Estimate Of Drug Likeness（Qed）
0.300