Chemical Components in the PDB

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SV2 : Summary

Code

SV2

One-letter code

X

Molecule name

[{2-[(guanine-9-yl)methyl]propane-1,3-diyl}bis(oxymethylene)]bis(phosphonic acid)

Systematic names

ProgramVersionName
ACDLabs 12.01 [{2-[(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)methyl]propane-1,3-diyl}bis(oxymethanediyl)]bis(phosphonic acid)
OpenEye OEToolkits 1.7.6 [2-[(2-azanyl-6-oxidanylidene-3H-purin-9-yl)methyl]-3-(phosphonomethoxy)propoxy]methylphosphonic acid

Formula

C11 H19 N5 O9 P2

Formal charge

0

Molecular weight

427.244 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)COCC(COCP(=O)(O)O)Cn1c2NC(=NC(=O)c2nc1)N
SMILES CACTVS 3.370 NC1=NC(=O)c2ncn(CC(COC[P](O)(O)=O)COC[P](O)(O)=O)c2N1
SMILES OpenEye OEToolkits 1.7.6 c1nc2c(n1CC(COCP(=O)(O)O)COCP(=O)(O)O)NC(=NC2=O)N
Canonical SMILES CACTVS 3.370 NC1=NC(=O)c2ncn(CC(COC[P](O)(O)=O)COC[P](O)(O)=O)c2N1
Canonical SMILES OpenEye OEToolkits 1.7.6 c1nc2c(n1CC(COCP(=O)(O)O)COCP(=O)(O)O)NC(=NC2=O)N

IUPAC InChI

InChI=1S/C11H19N5O9P2/c12-11-14-9-8(10(17)15-11)13-4-16(9)1-7(2-24-5-26(18,19)20)3-25-6-27(21,22)23/h4,7H,1-3,5-6H2,(H2,18,19,20)(H2,21,22,23)(H3,12,14,15,17)

IUPAC InChI key

VGXYLSOVNUSSKA-UHFFFAOYSA-N
SV2

wwPDB Information

Atom count

46 (27 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-02-20

Last modified at

2013-03-22

Status

Released

Obsoleted

Not Assigned



SV2 : Atoms of Molecule

Total Number of Atoms: 46
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OAE O OAE N N N 0 -2.622 2.929 -1.248
2 PAZ P PAZ N N N 0 -2.89 3.524 0.223
3 OAF O OAF N N N 0 -3.287 5.081 0.108
4 OAC O OAC N N N 0 -3.997 2.779 0.863
5 CAL C CAL N N N 0 -1.381 3.355 1.232
6 OAR O OAR N N N 0 -1.029 1.974 1.334
7 CAJ C CAJ N N N 0 -0.447 1.434 0.146
8 CAX C CAX N N N 0 -0.111 -0.043 0.369
9 CAK C CAK N N N 0 -1.404 -0.833 0.581
10 OAS O OAS N N N 0 -1.086 -2.183 0.925
11 CAM C CAM N N N 0 -2.226 -2.99 1.225
12 PBA P PBA N N N 0 -3.093 -3.415 -0.321
13 OAG O OAG N N N 0 -2.058 -4.1 -1.347
14 OAH O OAH N N N 0 -4.29 -4.444 0.0
15 OAD O OAD N N N 0 -3.649 -2.186 -0.929
16 CAN C CAN N N N 0 0.625 -0.589 -0.857
17 N9 N N9 N Y N 0 1.915 0.092 -0.995
18 C8 C C8 N Y N 0 2.174 1.175 -1.782
19 N7 N N7 N Y N 0 3.424 1.517 -1.654
20 C5 C C5 N Y N 0 4.028 0.676 -0.782
21 C4 C C4 N Y N 0 3.071 -0.237 -0.356
22 N3 N N3 N N N 0 3.433 -1.205 0.545
23 C2 C C2 N N N 0 4.708 -1.273 1.01
24 N2 N N2 N N N 0 5.03 -2.254 1.909
25 N1 N N1 N N N 0 5.646 -0.432 0.628
26 C6 C C6 N N N 0 5.386 0.554 -0.245
27 O6 O O6 N N N 0 6.264 1.331 -0.587
28 H1 H H1 N N N 0 -1.908 3.371 -1.727
29 H2 H H2 N N N 0 -4.083 5.246 -0.416
30 H3 H H3 N N N 0 -0.566 3.904 0.761
31 H4 H H4 N N N 0 -1.563 3.758 2.228
32 H5 H H5 N N N 0 -1.153 1.525 -0.679
33 H6 H H6 N N N 0 0.465 1.981 -0.093
34 H7 H H7 N N N 0 0.524 -0.142 1.249
35 H8 H H8 N N N 0 -1.979 -0.378 1.388
36 H9 H H9 N N N 0 -1.992 -0.821 -0.336
37 H10 H H10 N N N 0 -1.903 -3.904 1.724
38 H11 H H11 N N N 0 -2.9 -2.438 1.88
39 H12 H H12 N N N 0 -1.712 -4.951 -1.046
40 H13 H H13 N N N 0 -4.795 -4.714 -0.779
41 H14 H H14 N N N 0 0.79 -1.659 -0.734
42 H15 H H15 N N N 0 0.024 -0.414 -1.749
43 H16 H H16 N N N 0 1.454 1.672 -2.415
44 H17 H H17 N N N 0 2.774 -1.847 0.853
45 H19 H H19 N N N 0 5.913 -2.273 2.31
46 H18 H H18 N N N 0 4.375 -2.929 2.145



SV2 : Chemical Bonds

Total Number of Bonds: 47
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O6 C6 O C doub 1.22 N N
2 N7 C8 N C doub 1.3 N Y
3 N7 C5 N C sing 1.35 N Y
4 OAD PBA O P doub 1.48 N N
5 OAG PBA O P sing 1.61 N N
6 C8 N9 C N sing 1.36 N Y
7 C6 C5 C C sing 1.47 N N
8 C6 N1 C N sing 1.34 N N
9 C5 C4 C C doub 1.39 N Y
10 PBA OAH P O sing 1.61 N N
11 PBA CAM P C sing 1.82 N N
12 OAS CAM O C sing 1.43 N N
13 OAS CAK O C sing 1.43 N N
14 N1 C2 N C doub 1.32 N N
15 N9 C4 N C sing 1.36 N Y
16 N9 CAN N C sing 1.47 N N
17 C4 N3 C N sing 1.37 N N
18 CAK CAX C C sing 1.53 N N
19 CAN CAX C C sing 1.53 N N
20 C2 N3 C N sing 1.36 N N
21 C2 N2 C N sing 1.37 N N
22 CAX CAJ C C sing 1.53 N N
23 CAJ OAR C O sing 1.43 N N
24 OAR CAL O C sing 1.43 N N
25 CAL PAZ C P sing 1.82 N N
26 OAC PAZ O P doub 1.48 N N
27 PAZ OAE P O sing 1.61 N N
28 PAZ OAF P O sing 1.61 N N
29 OAE H1 O H sing 0.97 N N
30 OAF H2 O H sing 0.97 N N
31 CAL H3 C H sing 1.09 N N
32 CAL H4 C H sing 1.09 N N
33 CAJ H5 C H sing 1.09 N N
34 CAJ H6 C H sing 1.09 N N
35 CAX H7 C H sing 1.09 N N
36 CAK H8 C H sing 1.09 N N
37 CAK H9 C H sing 1.09 N N
38 CAM H10 C H sing 1.09 N N
39 CAM H11 C H sing 1.09 N N
40 OAG H12 O H sing 0.97 N N
41 OAH H13 O H sing 0.97 N N
42 CAN H14 C H sing 1.09 N N
43 CAN H15 C H sing 1.09 N N
44 C8 H16 C H sing 1.08 N N
45 N3 H17 N H sing 0.97 N N
46 N2 H18 N H sing 0.97 N N
47 N2 H19 N H sing 0.97 N N



SV2 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
SV2 4ijq Open in New Window Bound ligand 4 1
SV2 6aps Open in New Window Bound ligand 2 1