Biological Structure Resource | NDB | Structure Finder | à la mode | mmCIF

À La Mode Component ID: T_deoxyriboseC3endo_O3H_O5P_anti_+sc

Component name: (view abbreviated component mmCIF) (view full component mmCIF)

2'-deoxythymidine-5'-phosphate

Component description:

Model constructed for 2'-deoxythymidine-5'-phosphate from subcomponents for base, sugar and phosphate. The sugar is deoxyribose in the C3'-endo conformation, and geometries for the gamma torsion angle (synclinal), the chi torsion angle (antiperiplanar), and the C3*-O3* and C5*-O5* bonds are inserted from other models.

Component formula and formula weight:

H12 C10 N2 O8 P1 ( 319.2 grams/mole)

Modeled component diagram:


Modeled component formula and formula weight:

C10 N2 O8 P1 ( 307.1 grams/mole)

Component formal charge: -2


Component canonical SMILES string [Created by the Daylight Toolkit]:

Cc1cn(C2CC(O)C(COP(=O)([O-])[O-])O2)c(=O)[nH]c1=O

Component exchange SMILES string:

N1(C(N(C(C(=C1[H])C([H])([H])[H])=O)[H])=O)C2(C(C(C(C(OP(=O)([O-])[O-])([H])[H])(O2)[H])(O[H])[H])([H])[H])[H]

This model built from À La Mode sub-components:

Subcomponent ID Subcomponent Type Details
thy base Model constructed for thymine with an N1-glycosidic linkage.
deoxyribose_C3endo_O3H_O5P_+sc sugar Model constructed for 1'-amino-2'-deoxyribose in the C3'-endo conformation. the gamma torsion (synclinal), the corresponding O4*-C4*-C5*-O5* torsion, and the C3*-O3* and C5*-O5* bond geometries are inserted from other models.
PO4 phosphate n.a.


Stereochemical Features Table:


Chiral Center Neighbor U Neighbor V Neighbor W Volume [1] Volume E.S.D.
C3* C2* C4* O3* -2.5 0.10
C4* C3* O4* C5* 2.5 0.04


Chiral Center Neighbor U Neighbor V Neighbor W Out-of-plane Angle [2] Out-of-plane Angle E.S.D.
C3* C2* C4* O3* -51.7 2.87
C4* C3* O4* C5* 51.0 1.10

[1] Neighboring atoms U, V and W form vectors with the chiral center. The chiral volume is computed as (UxV)*W
[2] The out-of-plane angle is computed as 90.0 - ACOS(((UxV)*W)/(|UxV||W|))

Bond Distance Table:


Atom 1 Atom 2 Distance E.S.D. Type
N1 C2 1.3773 0.0086 sing
C2 N3 1.3734 0.0079 sing
N3 C4 1.3821 0.0084 sing
C4 C5 1.4446 0.0088 sing
C5 C6 1.3390 0.0064 doub
C6 N1 1.3796 0.0072 sing
C2 O2 1.2190 0.0079 doub
C4 O4 1.2282 0.0090 doub
C5 C5M 1.4977 0.0071 sing
N3 H3 n.a. n.a. sing
C6 H6 n.a. n.a. sing
C5M HC5MA n.a. n.a. sing
C5M HC5MB n.a. n.a. sing
C5M HC5MC n.a. n.a. sing
C1* C2* 1.5192 0.0069 sing
C2* C3* 1.5186 0.0110 sing
C3* C4* 1.5212 0.0081 sing
C4* O4* 1.4492 0.0060 sing
O4* C1* 1.4123 0.0065 sing
C3* O3* 1.4178 0.0067 sing
C4* C5* 1.5120 0.0117 sing
C5* O5* 1.4379 0.0099 sing
C1* HA1* n.a. n.a. sing
C2* HA2* n.a. n.a. sing
C2* HB2* n.a. n.a. sing
C3* HA3* n.a. n.a. sing
C4* HA4* n.a. n.a. sing
C5* HA5* n.a. n.a. sing
C5* HB5* n.a. n.a. sing
P O1P 1.4850 0.0170 doub
P O2P 1.4850 0.0170 sing
P O 1.4850 0.0170 sing
C1* N1 1.4947 0.0031 sing
P O5* 1.5930 0.0100 sing


Bond Angle Table:


Atom 1 Atom 2 Atom 3 Angle E.S.D.
C6 N1 C2 121.22 0.51
N1 C2 N3 114.54 0.59
C2 N3 C4 127.22 0.53
N3 C4 C5 115.18 0.61
C4 C5 C6 118.08 0.51
C5 C6 N1 123.63 0.56
N1 C2 O2 123.17 0.83
N3 C2 O2 122.28 0.63
N3 C4 O4 119.75 0.65
C5 C4 O4 125.07 0.74
C4 C5 C5M 118.99 0.57
C6 C5 C5M 122.91 0.60
C1* C2* C3* 102.80 0.51
C2* C3* C4* 102.26 0.57
C3* C4* O4* 104.79 0.66
C4* O4* C1* 110.21 0.61
O4* C1* C2* 107.01 0.63
C2* C3* O3* 112.71 2.71
C4* C3* O3* 112.97 1.78
C5* C4* C3* 115.64 1.14
C5* C4* O4* 109.36 0.32
O5* C5* C4* 111.28 1.54
O1P P O2P 119.60 1.50
O1P P O 108.30 3.20
O2P P O 107.30 3.20


Torsion Angle Table:


Atom 1 Atom 2 Atom 3 Atom 4 Angle E.S.D.
N1 C2 N3 C4 359.98 2.89
C2 N3 C4 C5 359.70 3.25
N3 C4 C5 C6 0.30 2.52
C4 C5 C6 N1 359.99 1.37
C5 C6 N1 C2 359.67 2.27
C6 N1 C2 N3 0.33 2.74
C6 N1 C2 O2 180.25 2.64
C4 N3 C2 O2 180.07 2.74
C2 N3 C4 O4 179.80 2.86
C6 C5 C4 O4 180.19 2.21
O4 C4 C5 C5M 0.26 2.16
N3 C4 C5 C5M 180.37 2.35
N1 C6 C5 C5M 179.92 1.53
C4* O4* C1* C2* 4.17 7.07
O4* C1* C2* C3* 335.52 5.35
C1* C2* C3* C4* 34.16 2.49
C2* C3* C4* O4* 327.62 3.09
C3* C4* O4* C1* 18.00 6.18
C2* C3* C4* C5* 207.16 3.23
C3* C4* C5* O5* 52.19 4.95
O3* C3* C4* C5* 85.70 4.91
O4* C4* C3* O3* 206.16 5.02
O4* C4* C5* O5* 293.22 4.75
C5* C4* O4* C1* 142.55 6.60
C1* C2* C3* O3* 155.80 4.77

Biological Structure Resource | NDB | Structure Finder | à la mode | mmCIF

ndbadmin@ndbserver.rutgers.edu
The Nucleic Acid Database Project
Rutgers, The State University of New Jersey