Chemical Components in the PDB

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VT0 : Summary

Code

VT0

One-letter code

X

Molecule name

{[(2-phenylthieno[2,3-d]pyrimidin-4-yl)amino]methylene}bis(phosphonic acid)

Systematic names

ProgramVersionName
ACDLabs 12.01 {[(2-phenylthieno[2,3-d]pyrimidin-4-yl)amino]methylene}bis(phosphonic acid)
OpenEye OEToolkits 2.0.6 [[(2-phenylthieno[2,3-d]pyrimidin-4-yl)amino]-phosphono-methyl]phosphonic acid

Formula

C13 H13 N3 O6 P2 S

Formal charge

0

Molecular weight

401.271 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)C(P(=O)(O)O)Nc1nc(nc2c1ccs2)c3ccccc3
SMILES CACTVS 3.385 O[P](O)(=O)C(Nc1nc(nc2sccc12)c3ccccc3)[P](O)(O)=O
SMILES OpenEye OEToolkits 2.0.6 c1ccc(cc1)c2nc(c3ccsc3n2)NC(P(=O)(O)O)P(=O)(O)O
Canonical SMILES CACTVS 3.385 O[P](O)(=O)C(Nc1nc(nc2sccc12)c3ccccc3)[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.6 c1ccc(cc1)c2nc(c3ccsc3n2)NC(P(=O)(O)O)P(=O)(O)O

IUPAC InChI

InChI=1S/C13H13N3O6P2S/c17-23(18,19)13(24(20,21)22)16-11-9-6-7-25-12(9)15-10(14-11)8-4-2-1-3-5-8/h1-7,13H,(H,14,15,16)(H2,17,18,19)(H2,20,21,22)

IUPAC InChI key

OVNNLIKSDUSVRR-UHFFFAOYSA-N
VT0

wwPDB Information

Atom count

38 (25 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-01-16

Last modified at

2018-08-31

Status

Released

Obsoleted

Not Assigned



VT0 : Atoms of Molecule

Total Number of Atoms: 38
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OAO O O1 N N N 0 2.615 -2.505 -0.973
2 PAL P P1 N N N 0 1.895 -1.224 -1.145
3 OAP O O2 N N N 0 2.622 -0.348 -2.283
4 OAN O O3 N N N 0 0.374 -1.518 -1.585
5 CAK C C1 N N N 0 1.905 -0.304 0.429
6 PAM P P2 N N N 0 3.626 0.029 0.926
7 OAR O O4 N N N 0 3.635 0.776 2.204
8 OAS O O5 N N N 0 4.41 -1.365 1.114
9 OAQ O O6 N N N 0 4.354 0.905 -0.212
10 NAJ N N1 N N N 0 1.191 0.964 0.258
11 C4 C C2 N Y N 0 -0.19 0.976 0.188
12 N3 N N2 N Y N 0 -0.876 -0.151 0.274
13 C5 C C3 N Y N 0 -0.892 2.201 0.028
14 CAC C C4 N Y N 0 -0.397 3.559 -0.086
15 CAD C C5 N Y N 0 -1.332 4.479 -0.226
16 SAE S S1 N Y N 0 -2.934 3.768 -0.233
17 C6 C C6 N Y N 0 -2.288 2.145 -0.036
18 N1 N N3 N Y N 0 -2.899 0.959 0.055
19 C2 C C7 N Y N 0 -2.204 -0.154 0.208
20 CAT C C8 N Y N 0 -2.927 -1.444 0.31
21 CAU C C9 N Y N 0 -4.319 -1.474 0.244
22 CAV C C10 N Y N 0 -4.986 -2.678 0.339
23 CAW C C11 N Y N 0 -4.276 -3.855 0.5
24 CAX C C12 N Y N 0 -2.894 -3.831 0.566
25 CAY C C13 N Y N 0 -2.216 -2.634 0.466
26 H1 H H1 N N N 0 2.654 -0.776 -3.15
27 H2 H H2 N N N 0 -0.159 -0.722 -1.716
28 H3 H H3 N N N 0 1.412 -0.897 1.199
29 H4 H H4 N N N 0 5.335 -1.263 1.379
30 H5 H H5 N N N 0 4.385 0.477 -1.078
31 H6 H H6 N N N 0 1.688 1.795 0.194
32 H8 H H8 N N N 0 0.656 3.798 -0.058
33 H9 H H9 N N N 0 -1.135 5.537 -0.325
34 H12 H H12 N N N 0 -4.874 -0.556 0.119
35 H13 H H13 N N N 0 -6.064 -2.703 0.288
36 H14 H H14 N N N 0 -4.802 -4.795 0.574
37 H15 H H15 N N N 0 -2.345 -4.753 0.691
38 H16 H H16 N N N 0 -1.137 -2.617 0.513



VT0 : Chemical Bonds

Total Number of Bonds: 40
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OAO PAL O P doub 1.48 N N
2 PAL OAP P O sing 1.61 N N
3 PAL OAN P O sing 1.61 N N
4 PAL CAK P C sing 1.82 N N
5 CAK PAM C P sing 1.82 N N
6 CAK NAJ C N sing 1.47 N N
7 PAM OAR P O doub 1.48 N N
8 PAM OAS P O sing 1.61 N N
9 PAM OAQ P O sing 1.61 N N
10 NAJ C4 N C sing 1.38 N N
11 C4 N3 C N doub 1.32 N Y
12 C4 C5 C C sing 1.42 N Y
13 N3 C2 N C sing 1.33 N Y
14 C5 CAC C C sing 1.45 N Y
15 C5 C6 C C doub 1.4 N Y
16 CAC CAD C C doub 1.32 N Y
17 CAD SAE C S sing 1.75 N Y
18 SAE C6 S C sing 1.76 N Y
19 C6 N1 C N sing 1.34 N Y
20 N1 C2 N C doub 1.32 N Y
21 C2 CAT C C sing 1.48 N N
22 CAT CAU C C doub 1.39 N Y
23 CAT CAY C C sing 1.39 N Y
24 CAU CAV C C sing 1.38 N Y
25 CAV CAW C C doub 1.38 N Y
26 CAW CAX C C sing 1.38 N Y
27 CAX CAY C C doub 1.38 N Y
28 OAP H1 O H sing 0.97 N N
29 OAN H2 O H sing 0.97 N N
30 CAK H3 C H sing 1.09 N N
31 OAS H4 O H sing 0.97 N N
32 OAQ H5 O H sing 0.97 N N
33 NAJ H6 N H sing 0.97 N N
34 CAC H8 C H sing 1.08 N N
35 CAD H9 C H sing 1.08 N N
36 CAU H12 C H sing 1.08 N N
37 CAV H13 C H sing 1.08 N N
38 CAW H14 C H sing 1.08 N N
39 CAX H15 C H sing 1.08 N N
40 CAY H16 C H sing 1.08 N N



VT0 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
VT0 6c56 Open in New Window Bound ligand 1 1