Chemical Components in the PDB

pdbe.org/chem
spacer

6C6 : Summary

Code

6C6

One-letter code

X

Molecule name

N-cyclopentyladenosine 5'-(dihydrogen phosphate)

Systematic names

ProgramVersionName
ACDLabs 12.01 N-cyclopentyladenosine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 1.7.6 [(2R,3S,4R,5R)-5-[6-(cyclopentylamino)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate

Formula

C15 H22 N5 O7 P

Formal charge

0

Molecular weight

415.338 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OCC4OC(n2cnc1c(ncnc12)NC3CCCC3)C(O)C4O
SMILES CACTVS 3.370 O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)n2cnc3c(NC4CCCC4)ncnc23
SMILES OpenEye OEToolkits 1.7.6 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)NC4CCCC4
Canonical SMILES CACTVS 3.370 O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3c(NC4CCCC4)ncnc23
Canonical SMILES OpenEye OEToolkits 1.7.6 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)NC4CCCC4

IUPAC InChI

InChI=1S/C15H22N5O7P/c21-11-9(5-26-28(23,24)25)27-15(12(11)22)20-7-18-10-13(16-6-17-14(10)20)19-8-3-1-2-4-8/h6-9,11-12,15,21-22H,1-5H2,(H,16,17,19)(H2,23,24,25)/t9-,11-,12-,15-/m1/s1

IUPAC InChI key

ZLXWBMMFOMQXRH-SDBHATRESA-N
6C6

wwPDB Information

Atom count

50 (28 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-07-13

Last modified at

2012-12-28

Status

Released

Obsoleted

Not Assigned



6C6 : Atoms of Molecule

Total Number of Atoms: 50
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C65 C C65 N N N 0 -6.926 0.097 -0.888
2 C64 C C64 N N N 0 -8.313 0.736 -1.079
3 C63 C C63 N N N 0 -8.387 1.929 -0.105
4 C62 C C62 N N N 0 -6.906 2.306 0.148
5 C61 C C61 N N N 0 -6.205 0.925 0.195
6 N6 N N6 N N N 0 -4.781 1.061 -0.125
7 C6 C C6 N Y N 0 -3.875 0.124 0.339
8 N1 N N1 N Y N 0 -4.28 -0.909 1.072
9 C2 C C2 N Y N 0 -3.422 -1.808 1.519
10 N3 N N3 N Y N 0 -2.131 -1.738 1.27
11 C4 C C4 N Y N 0 -1.634 -0.741 0.546
12 C5 C C5 N Y N 0 -2.507 0.238 0.042
13 N7 N N7 N Y N 0 -1.754 1.122 -0.656
14 C8 C C8 N Y N 0 -0.506 0.754 -0.618
15 N9 N N9 N Y N 0 -0.379 -0.386 0.119
16 C1' C C1* R N N 0 0.866 -1.108 0.391
17 O4' O O4* N N N 0 1.997 -0.216 0.286
18 C2' C C2* R N N 0 1.11 -2.184 -0.69
19 O2' O O2* N N N 0 0.688 -3.467 -0.223
20 C3' C C3* S N N 0 2.64 -2.162 -0.903
21 O3' O O3* N N N 0 3.21 -3.43 -0.575
22 C4' C C4* R N N 0 3.139 -1.075 0.074
23 C5' C C5* N N N 0 4.291 -0.284 -0.552
24 O5' O O5* N N N 0 4.814 0.636 0.409
25 PA P PA N N N 0 6.037 1.633 0.091
26 OA2 O OA2 N N N 0 7.372 0.775 -0.179
27 OA3 O OA3 N N N 0 5.718 2.44 -1.107
28 OA1 O OA1 N N N 0 6.273 2.61 1.349
29 H1 H H1 N N N 0 -7.033 -0.936 -0.559
30 H2 H H2 N N N 0 -6.366 0.136 -1.822
31 H3 H H3 N N N 0 -8.425 1.085 -2.106
32 H4 H H4 N N N 0 -9.093 0.012 -0.844
33 H5 H H5 N N N 0 -8.92 2.763 -0.562
34 H6 H H6 N N N 0 -8.869 1.632 0.827
35 H7 H H7 N N N 0 -6.515 2.908 -0.672
36 H8 H H8 N N N 0 -6.796 2.828 1.098
37 H9 H H9 N N N 0 -6.334 0.465 1.175
38 H10 H H10 N N N 0 -4.474 1.808 -0.662
39 H11 H H11 N N N 0 -3.793 -2.631 2.111
40 H12 H H12 N N N 0 0.309 1.279 -1.093
41 H13 H H13 N N N 0 0.831 -1.563 1.381
42 H14 H H14 N N N 0 0.592 -1.923 -1.613
43 H15 H H15 N N N 0 0.873 -4.19 -0.838
44 H16 H H16 N N N 0 2.879 -1.89 -1.931
45 H17 H H17 N N N 0 2.885 -4.161 -1.119
46 H18 H H18 N N N 0 3.455 -1.526 1.015
47 H19 H H19 N N N 0 5.077 -0.972 -0.862
48 H20 H H20 N N N 0 3.925 0.265 -1.419
49 H21 H H21 N N N 0 7.642 0.221 0.566
50 H22 H H22 N N N 0 6.997 3.239 1.228



6C6 : Chemical Bonds

Total Number of Bonds: 53
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C2 N1 C N doub 1.32 N Y
2 C2 N3 C N sing 1.32 N Y
3 O2' C2' O C sing 1.43 N N
4 N1 C6 N C sing 1.33 N Y
5 N3 C4 N C doub 1.33 N Y
6 O3' C3' O C sing 1.43 N N
7 C2' C3' C C sing 1.54 N N
8 C2' C1' C C sing 1.54 N N
9 C3' C4' C C sing 1.54 N N
10 C6 N6 C N sing 1.38 N N
11 C6 C5 C C doub 1.4 N Y
12 C4 C5 C C sing 1.41 N Y
13 C4 N9 C N sing 1.37 N Y
14 N6 C61 N C sing 1.47 N N
15 C63 C62 C C sing 1.55 N N
16 C63 C64 C C sing 1.54 N N
17 C5 N7 C N sing 1.35 N Y
18 C1' N9 C N sing 1.46 N N
19 C1' O4' C O sing 1.44 N N
20 N9 C8 N C sing 1.36 N Y
21 C62 C61 C C sing 1.55 N N
22 C4' O4' C O sing 1.44 N N
23 C4' C5' C C sing 1.53 N N
24 C64 C65 C C sing 1.54 N N
25 C61 C65 C C sing 1.54 N N
26 N7 C8 N C doub 1.3 N Y
27 C5' O5' C O sing 1.43 N N
28 O5' PA O P sing 1.61 N N
29 OA3 PA O P doub 1.48 N N
30 OA1 PA O P sing 1.61 N N
31 PA OA2 P O sing 1.61 N N
32 C65 H1 C H sing 1.09 N N
33 C65 H2 C H sing 1.09 N N
34 C64 H3 C H sing 1.09 N N
35 C64 H4 C H sing 1.09 N N
36 C63 H5 C H sing 1.09 N N
37 C63 H6 C H sing 1.09 N N
38 C62 H7 C H sing 1.09 N N
39 C62 H8 C H sing 1.09 N N
40 C61 H9 C H sing 1.09 N N
41 N6 H10 N H sing 0.97 N N
42 C2 H11 C H sing 1.08 N N
43 C8 H12 C H sing 1.08 N N
44 C1' H13 C H sing 1.09 N N
45 C2' H14 C H sing 1.09 N N
46 O2' H15 O H sing 0.97 N N
47 C3' H16 C H sing 1.09 N N
48 O3' H17 O H sing 0.97 N N
49 C4' H18 C H sing 1.09 N N
50 C5' H19 C H sing 1.09 N N
51 C5' H20 C H sing 1.09 N N
52 OA2 H21 O H sing 0.97 N N
53 OA1 H22 O H sing 0.97 N N



6C6 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
6C6 4fyi Open in New Window Bound ligand 4 1
6C6 4kxl Open in New Window Bound ligand 4 1