Chemical Components in the PDB

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WPG : Summary

Code

WPG

One-letter code

X

Molecule name

(3-{(3R,4R)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-4-[(2R)-2-hydroxy-2-phosphonoethoxy]pyrrolidin-1-yl}-3-oxopropy l)phosphonic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 (3-{(3R,4R)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-4-[(2R)-2-hydroxy-2-phosphonoethoxy]pyrrolidin-1-yl}-3-oxopropyl)phosphonic acid
OpenEye OEToolkits 2.0.4 [3-[(3~{R},4~{R})-3-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[(2~{R})-2-oxidanyl-2-phosphono-ethoxy]pyrrolidin-1-yl]-3-oxidanylidene-propyl]phosphonic acid

Formula

C14 H22 N6 O10 P2

Formal charge

0

Molecular weight

496.306 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 c12c(C(=O)NC(N)=N1)ncn2C3C(OCC(P(=O)(O)O)O)CN(C3)C(=O)CCP(O)(O)=O
SMILES CACTVS 3.385 NC1=Nc2n(cnc2C(=O)N1)[CH]3CN(C[CH]3OC[CH](O)[P](O)(O)=O)C(=O)CC[P](O)(O)=O
SMILES OpenEye OEToolkits 2.0.4 c1nc2c(n1C3CN(CC3OCC(O)P(=O)(O)O)C(=O)CCP(=O)(O)O)N=C(NC2=O)N
Canonical SMILES CACTVS 3.385 NC1=Nc2n(cnc2C(=O)N1)[C@@H]3CN(C[C@H]3OC[C@H](O)[P](O)(O)=O)C(=O)CC[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.4 c1nc2c(n1[C@@H]3CN(C[C@H]3OC[C@H](O)P(=O)(O)O)C(=O)CCP(=O)(O)O)N=C(NC2=O)N

IUPAC InChI

InChI=1S/C14H22N6O10P2/c15-14-17-12-11(13(23)18-14)16-6-20(12)7-3-19(9(21)1-2-31(24,25)26)4-8(7)30-5-10(22)32(27,28)29/h6-8,10,22H,1-5H2,(H2,24,25,26)(H2,27,28,29)(H3,15,17,18,23)/t7-,8-,10-/m1/s1

IUPAC InChI key

RBYFDIJTTUISNF-NQMVMOMDSA-N
WPG

wwPDB Information

Atom count

54 (32 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2016-01-14

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



WPG : Atoms of Molecule

Total Number of Atoms: 54
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 N Y N 0 3.329 1.655 -0.177
2 C5 C C2 N Y N 0 4.047 2.396 0.767
3 C6 C C3 N N N 0 5.437 2.572 0.575
4 C8 C C4 N Y N 0 1.978 2.368 1.412
5 N1 N N1 N N N 0 6.01 2.015 -0.515
6 N2 N N2 N N N 0 5.865 0.748 -2.498
7 N3 N N3 N N N 0 3.964 1.132 -1.233
8 OAI O O1 N N N 0 -0.684 -4.601 0.339
9 PBF P P1 N N N 0 0.718 -4.342 -0.059
10 OAJ O O2 N N N 0 1.463 -5.741 -0.343
11 OAE O O3 N N N 0 0.74 -3.441 -1.393
12 CAZ C C5 R N N 0 1.577 -3.458 1.285
13 OAF O O4 N N N 0 2.931 -3.208 0.901
14 CAN C C6 N N N 0 0.87 -2.129 1.555
15 OAT O O5 N N N 0 0.889 -1.33 0.371
16 CBA C C7 R N N 0 0.25 -0.06 0.516
17 CAO C C8 N N N 0 -1.201 -0.102 -0.025
18 NBC N N4 N N N 0 -1.51 1.293 -0.386
19 CAU C C9 N N N 0 -2.744 1.83 -0.461
20 OAB O O6 N N N 0 -2.881 2.995 -0.768
21 CAL C C10 N N N 0 -3.954 0.982 -0.162
22 CAM C C11 N N N 0 -5.22 1.827 -0.319
23 PBE P P2 N N N 0 -6.683 0.802 0.043
24 OAG O O7 N N N 0 -6.809 -0.363 -1.062
25 OAH O O8 N N N 0 -6.541 0.195 1.385
26 OAD O O9 N N N 0 -8.005 1.721 0.007
27 CAP C C12 N N N 0 -0.25 2.003 -0.65
28 CBB C C13 R N N 0 0.899 0.999 -0.415
29 N9 N N5 N Y N 0 2.029 1.651 0.251
30 C2 C C14 N N N 0 5.257 1.303 -1.401
31 O6 O O10 N N N 0 6.102 3.211 1.372
32 N7 N N6 N Y N 0 3.167 2.8 1.715
33 H1 H H1 N N N 0 1.086 2.544 1.994
34 H2 H H2 N N N 0 5.342 0.238 -3.136
35 H3 H H3 N N N 0 6.818 0.866 -2.636
36 H5 H H5 N N N 0 1.058 -6.265 -1.048
37 H6 H H6 N N N 0 1.628 -3.232 -1.712
38 H7 H H7 N N N 0 1.563 -4.068 2.188
39 H8 H H8 N N N 0 3.02 -2.67 0.102
40 H9 H H9 N N N 0 -0.163 -2.32 1.848
41 H10 H H10 N N N 0 1.383 -1.601 2.358
42 H11 H H11 N N N 0 0.271 0.269 1.555
43 H12 H H12 N N N 0 -1.259 -0.743 -0.905
44 H13 H H13 N N N 0 -1.883 -0.457 0.747
45 H14 H H14 N N N 0 -3.99 0.142 -0.856
46 H15 H H15 N N N 0 -3.891 0.607 0.859
47 H16 H H16 N N N 0 -5.184 2.667 0.375
48 H17 H H17 N N N 0 -5.282 2.202 -1.34
49 H18 H H18 N N N 0 -6.905 -0.037 -1.967
50 H19 H H19 N N N 0 -8.823 1.24 0.191
51 H20 H H20 N N N 0 -0.231 2.353 -1.682
52 H21 H H21 N N N 0 -0.15 2.847 0.032
53 H22 H H22 N N N 0 1.213 0.545 -1.355
54 H23 H H23 N N N 0 6.962 2.122 -0.668



WPG : Chemical Bonds

Total Number of Bonds: 56
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OAH PBE O P doub 1.48 N N
2 CAM CAL C C sing 1.53 N N
3 CAM PBE C P sing 1.82 N N
4 CAL CAU C C sing 1.51 N N
5 PBE OAD P O sing 1.61 N N
6 PBE OAG P O sing 1.61 N N
7 CAU OAB C O doub 1.21 N N
8 CAU NBC C N sing 1.35 N N
9 OAI PBF O P doub 1.48 N N
10 OAF CAZ O C sing 1.43 N N
11 NBC CAO N C sing 1.47 N N
12 NBC CAP N C sing 1.47 N N
13 CAO CBA C C sing 1.55 N N
14 CAZ PBF C P sing 1.82 N N
15 CAZ CAN C C sing 1.53 N N
16 PBF OAE P O sing 1.61 N N
17 PBF OAJ P O sing 1.61 N N
18 CAP CBB C C sing 1.54 N N
19 CBA OAT C O sing 1.43 N N
20 CBA CBB C C sing 1.55 N N
21 OAT CAN O C sing 1.43 N N
22 CBB N9 C N sing 1.46 N N
23 N9 C8 N C sing 1.37 N Y
24 N9 C4 N C sing 1.37 N Y
25 N3 C4 N C sing 1.34 N N
26 N3 C2 N C doub 1.32 N N
27 C8 N7 C N doub 1.3 N Y
28 C4 C5 C C doub 1.4 N Y
29 N2 C2 N C sing 1.37 N N
30 C2 N1 C N sing 1.36 N N
31 N7 C5 N C sing 1.36 N Y
32 C5 C6 C C sing 1.41 N N
33 N1 C6 N C sing 1.35 N N
34 C6 O6 C O doub 1.22 N N
35 C8 H1 C H sing 1.08 N N
36 N2 H2 N H sing 0.97 N N
37 N2 H3 N H sing 0.97 N N
38 OAJ H5 O H sing 0.97 N N
39 OAE H6 O H sing 0.97 N N
40 CAZ H7 C H sing 1.09 N N
41 OAF H8 O H sing 0.97 N N
42 CAN H9 C H sing 1.09 N N
43 CAN H10 C H sing 1.09 N N
44 CBA H11 C H sing 1.09 N N
45 CAO H12 C H sing 1.09 N N
46 CAO H13 C H sing 1.09 N N
47 CAL H14 C H sing 1.09 N N
48 CAL H15 C H sing 1.09 N N
49 CAM H16 C H sing 1.09 N N
50 CAM H17 C H sing 1.09 N N
51 OAG H18 O H sing 0.97 N N
52 OAD H19 O H sing 0.97 N N
53 CAP H20 C H sing 1.09 N N
54 CAP H21 C H sing 1.09 N N
55 CBB H22 C H sing 1.09 N N
56 N1 H23 N H sing 0.97 N N



WPG : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
WPG 6bnj Open in New Window Bound ligand 4 1