Chemical Components in the PDB

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3ZE : Summary

Code

3ZE

One-letter code

X

Molecule name

{2-[(3S,4R)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-4-hydroxypyrrolidin-1-yl]-2-oxoethyl}phosphonic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 {2-[(3S,4R)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-4-hydroxypyrrolidin-1-yl]-2-oxoethyl}phosphonic acid
OpenEye OEToolkits 1.7.6 [2-[(3S,4R)-3-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-oxidanyl-pyrrolidin-1-yl]-2-oxidanylidene-ethyl]phosphonic acid

Formula

C11 H15 N6 O6 P

Formal charge

0

Molecular weight

358.247 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(N3CC(n1c2N=C(N)NC(=O)c2nc1)C(O)C3)CP(=O)(O)O
SMILES CACTVS 3.385 NC1=Nc2n(cnc2C(=O)N1)[CH]3CN(C[CH]3O)C(=O)C[P](O)(O)=O
SMILES OpenEye OEToolkits 1.7.6 c1nc2c(n1C3CN(CC3O)C(=O)CP(=O)(O)O)N=C(NC2=O)N
Canonical SMILES CACTVS 3.385 NC1=Nc2n(cnc2C(=O)N1)[C@H]3CN(C[C@H]3O)C(=O)C[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 c1nc2c(n1[C@H]3CN(C[C@H]3O)C(=O)CP(=O)(O)O)N=C(NC2=O)N

IUPAC InChI

InChI=1S/C11H15N6O6P/c12-11-14-9-8(10(20)15-11)13-4-17(9)5-1-16(2-6(5)18)7(19)3-24(21,22)23/h4-6,18H,1-3H2,(H2,21,22,23)(H3,12,14,15,20)/t5-,6+/m0/s1

IUPAC InChI key

PIHCTBQWWHFPNB-NTSWFWBYSA-N
3ZE

wwPDB Information

Atom count

39 (24 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-12-16

Last modified at

2014-12-19

Status

Released

Obsoleted

Not Assigned



3ZE : Atoms of Molecule

Total Number of Atoms: 39
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C4 N Y N 0 3.103 0.11 0.058
2 C5 C C5 N Y N 0 3.907 -0.934 -0.413
3 C6 C C6 N N N 0 5.3 -0.717 -0.528
4 C8 C C8 N Y N 0 1.866 -1.662 -0.377
5 N1 N N1 N N N 0 5.792 0.492 -0.177
6 N2 N N2 N N N 0 5.485 2.687 0.626
7 N3 N N3 N N N 0 3.662 1.28 0.388
8 OAF O OAF N N N 0 -6.617 0.111 0.645
9 PAX P PAX N N N 0 -5.22 -0.089 -0.131
10 OAG O OAG N N N 0 -4.57 -1.5 0.289
11 OAD O OAD N N N 0 -5.461 -0.072 -1.592
12 CAI C CAI N N N 0 -4.079 1.262 0.312
13 CAO C CAO N N N 0 -2.819 1.144 -0.506
14 OAB O OAB N N N 0 -2.8 1.544 -1.65
15 NAV N NAV N N N 0 -1.714 0.594 0.035
16 CAK C CAK N N N 0 -0.418 0.423 -0.647
17 CAJ C CAJ N N N 0 -1.599 0.071 1.404
18 CAT C CAT R N N 0 -0.151 -0.431 1.583
19 OAE O OAE N N N 0 -0.071 -1.838 1.347
20 CAU C CAU S N N 0 0.625 0.356 0.496
21 N9 N N9 N Y N 0 1.823 -0.374 0.072
22 C2 C C2 N N N 0 4.957 1.47 0.277
23 O6 O O6 N N N 0 6.039 -1.598 -0.934
24 N7 N N7 N Y N 0 3.092 -1.987 -0.666
25 H1 H H1 N N N 0 1.011 -2.314 -0.477
26 H2 H H2 N N N 0 6.744 0.665 -0.247
27 H3 H H3 N N N 0 4.904 3.393 0.949
28 H4 H H4 N N N 0 6.44 2.842 0.549
29 H5 H H5 N N N 0 -7.273 -0.573 0.456
30 H6 H H6 N N N 0 -4.385 -1.582 1.234
31 H7 H H7 N N N 0 -4.556 2.221 0.11
32 H8 H H8 N N N 0 -3.832 1.195 1.372
33 H9 H H9 N N N 0 -0.411 -0.504 -1.221
34 H10 H H10 N N N 0 -0.216 1.274 -1.296
35 H11 H H11 N N N 0 -1.808 0.863 2.123
36 H12 H H12 N N N 0 -2.297 -0.754 1.546
37 H13 H H13 N N N 0 0.223 -0.184 2.576
38 H14 H H14 N N N 0 -0.602 -2.37 1.955
39 H15 H H15 N N N 0 0.883 1.355 0.849



3ZE : Chemical Bonds

Total Number of Bonds: 41
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OAD PAX O P doub 1.48 N N
2 OAF PAX O P sing 1.61 N N
3 PAX OAG P O sing 1.61 N N
4 PAX CAI P C sing 1.82 N N
5 OAB CAO O C doub 1.21 N N
6 CAI CAO C C sing 1.51 N N
7 CAO NAV C N sing 1.35 N N
8 NAV CAJ N C sing 1.47 N N
9 NAV CAK N C sing 1.47 N N
10 CAJ CAT C C sing 1.54 N N
11 CAK CAU C C sing 1.55 N N
12 OAE CAT O C sing 1.43 N N
13 CAT CAU C C sing 1.55 N N
14 CAU N9 C N sing 1.47 N N
15 C8 N9 C N sing 1.36 N Y
16 C8 N7 C N doub 1.3 N Y
17 N9 C4 N C sing 1.37 N Y
18 N7 C5 N C sing 1.36 N Y
19 C4 C5 C C doub 1.4 N Y
20 C4 N3 C N sing 1.34 N N
21 C5 C6 C C sing 1.41 N N
22 N3 C2 N C doub 1.31 N N
23 C6 O6 C O doub 1.22 N N
24 C6 N1 C N sing 1.35 N N
25 C2 N1 C N sing 1.36 N N
26 C2 N2 C N sing 1.37 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 OAF H5 O H sing 0.97 N N
32 OAG H6 O H sing 0.97 N N
33 CAI H7 C H sing 1.09 N N
34 CAI H8 C H sing 1.09 N N
35 CAK H9 C H sing 1.09 N N
36 CAK H10 C H sing 1.09 N N
37 CAJ H11 C H sing 1.09 N N
38 CAJ H12 C H sing 1.09 N N
39 CAT H13 C H sing 1.09 N N
40 OAE H14 O H sing 0.97 N N
41 CAU H15 C H sing 1.09 N N



3ZE : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
3ZE 4jls Open in New Window Bound ligand 8 1