Chemical Components in the PDB

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1TW : Summary

Code

1TW

One-letter code

X

Molecule name

2-amino-9-(2-Se-methyl-5-O-phosphono-2-seleno-beta-D-arabinofuranosyl)-1,9-dihydro-6H-purin-6-one

Systematic names

ProgramVersionName
ACDLabs 12.01 2-amino-9-(2-Se-methyl-5-O-phosphono-2-seleno-beta-D-arabinofuranosyl)-1,9-dihydro-6H-purin-6-one
OpenEye OEToolkits 1.7.6 [(2R,3R,4S,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-methylselanyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C11 H16 N5 O7 P Se

Formal charge

0

Molecular weight

440.208 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C([Se]C)C3O
SMILES CACTVS 3.370 C[Se][CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1n2cnc3C(=O)NC(=Nc23)N
SMILES OpenEye OEToolkits 1.7.6 C[Se]C1C(C(OC1n2cnc3c2N=C(NC3=O)N)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.370 C[Se][C@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1n2cnc3C(=O)NC(=Nc23)N
Canonical SMILES OpenEye OEToolkits 1.7.6 C[Se][C@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2N=C(NC3=O)N)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C11H16N5O7PSe/c1-25-7-6(17)4(2-22-24(19,20)21)23-10(7)16-3-13-5-8(16)14-11(12)15-9(5)18/h3-4,6-7,10,17H,2H2,1H3,(H2,19,20,21)(H3,12,14,15,18)/t4-,6-,7+,10-/m1/s1

IUPAC InChI key

VGEIDTKNQDSGED-UHTZMRCNSA-N
1TW

wwPDB Information

Atom count

41 (25 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-06-03

Last modified at

2013-07-12

Status

Released

Obsoleted

Not Assigned



1TW : Atoms of Molecule

Total Number of Atoms: 41
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1' C C1' R N N 0 -0.322 -0.119 -0.893
2 C2 C C2 N N N 0 -4.68 -0.959 -1.495
3 C2' C C2' S N N 0 -0.294 1.419 -0.756
4 C3' C C3' R N N 0 1.207 1.776 -0.841
5 C4 C C4 N Y N 0 -2.67 -0.886 -0.357
6 C4' C C4' R N N 0 1.908 0.412 -1.02
7 C5 C C5 N Y N 0 -3.275 -1.448 0.774
8 C5' C C5' N N N 0 3.232 0.388 -0.253
9 C6 C C6 N N N 0 -4.653 -1.761 0.719
10 C8 C C8 N Y N 0 -1.188 -1.121 1.257
11 CA' C CA' N N N 0 -0.746 3.906 0.906
12 H1 H H1 N N N 0 -0.256 -1.096 1.803
13 H10 H H10 N N N 0 1.538 2.258 0.078
14 H11 H H11 N N N 0 2.385 2.874 -2.07
15 H12 H H12 N N N 0 2.077 0.207 -2.077
16 H13 H H13 N N N 0 3.849 1.229 -0.569
17 H14 H H14 N N N 0 3.034 0.464 0.816
18 H15 H H15 N N Y 0 6.567 -0.178 -1.389
19 H16 H H16 N N N 0 6.612 -2.986 0.053
20 H2 H H2 N N N 0 -6.269 -1.717 -0.488
21 H3 H H3 N N N 0 -6.331 -0.929 -2.689
22 H4 H H4 N N N 0 -4.941 -0.323 -3.414
23 H5 H H5 N N N 0 -0.495 -0.407 -1.93
24 H6 H H6 N N N 0 -0.845 1.887 -1.571
25 H7 H H7 N N N 0 -1.117 4.361 1.824
26 H8 H H8 N N N 0 0.319 4.112 0.802
27 H9 H H9 N N N 0 -1.281 4.322 0.052
28 N1 N N1 N N N 0 -5.324 -1.508 -0.426
29 N2 N N2 N N N 0 -5.386 -0.713 -2.645
30 N3 N N3 N N N 0 -3.401 -0.658 -1.455
31 N7 N N7 N Y N 0 -2.317 -1.566 1.725
32 N9 N N9 N Y N 0 -1.357 -0.69 -0.027
33 O3' O O3' N N N 0 1.457 2.619 -1.968
34 O4' O O4' N N N 0 0.987 -0.552 -0.463
35 O5' O O5' N N N 0 3.918 -0.835 -0.525
36 O6 O O6 N N N 0 -5.221 -2.252 1.68
37 OP1 O OP1 N N N 0 5.267 -1.102 1.592
38 OP2 O OP2 N N N 0 5.759 -2.699 -0.3
39 OP3 O OP3 N N Y 0 6.459 -0.168 -0.428
40 P P P N N N 0 5.349 -1.199 0.117
41 SE2 SE SE2 N N N 0 -1.033 1.968 0.975



1TW : Chemical Bonds

Total Number of Bonds: 43
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O3' C3' O C sing 1.43 N N
2 CA' SE2 C SE sing 1.96 N N
3 C2' C3' C C sing 1.55 N N
4 C2' SE2 C SE sing 1.96 N N
5 C2' C1' C C sing 1.54 N N
6 C3' C4' C C sing 1.54 N N
7 C1' N9 C N sing 1.47 N N
8 C1' O4' C O sing 1.44 N N
9 N2 C2 N C sing 1.37 N N
10 N3 C2 N C doub 1.31 N N
11 N3 C4 N C sing 1.34 N N
12 N9 C4 N C sing 1.37 N Y
13 N9 C8 N C sing 1.36 N Y
14 C2 N1 C N sing 1.36 N N
15 C4 C5 C C doub 1.4 N Y
16 C4' O4' C O sing 1.44 N N
17 C4' C5' C C sing 1.53 N N
18 C8 N7 C N doub 1.3 N Y
19 N1 C6 N C sing 1.35 N N
20 C5 N7 C N sing 1.36 N Y
21 C5 C6 C C sing 1.41 N N
22 C6 O6 C O doub 1.22 N N
23 O5' C5' O C sing 1.43 N N
24 O5' P O P sing 1.61 N N
25 OP1 P O P doub 1.48 N N
26 P OP2 P O sing 1.61 N N
27 C8 H1 C H sing 1.08 N N
28 N1 H2 N H sing 0.97 N N
29 N2 H3 N H sing 0.97 N N
30 N2 H4 N H sing 0.97 N N
31 C1' H5 C H sing 1.09 N N
32 C2' H6 C H sing 1.09 N N
33 CA' H7 C H sing 1.09 N N
34 CA' H8 C H sing 1.09 N N
35 CA' H9 C H sing 1.09 N N
36 C3' H10 C H sing 1.09 N N
37 O3' H11 O H sing 0.97 N N
38 C4' H12 C H sing 1.09 N N
39 C5' H13 C H sing 1.09 N N
40 C5' H14 C H sing 1.09 N N
41 OP2 H16 O H sing 0.97 N N
42 P OP3 P O sing 1.61 N N
43 OP3 H15 O H sing 0.97 N N



1TW : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
1TW 4kw0 Open in New Window Polymer component 2 1