Chemical Components in the PDB

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9YP : Summary

Code

9YP

One-letter code

X

Molecule name

{[(2R)-2-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)methyl]-3-(2-phosphonoethoxy)propoxy]methyl}phosphonic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 {[(2R)-2-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)methyl]-3-(2-phosphonoethoxy)propoxy]methyl}phosphonic acid
OpenEye OEToolkits 2.0.6 [(2~{R})-2-[(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)methyl]-3-(2-phosphonoethoxy)propoxy]methylphosphonic acid

Formula

C12 H21 N5 O9 P2

Formal charge

0

Molecular weight

441.271 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 OP(O)(=O)CCOCC(COCP(O)(=O)O)Cn2c1N=C(N)NC(c1nc2)=O
SMILES CACTVS 3.385 NC1=Nc2n(C[CH](COCC[P](O)(O)=O)COC[P](O)(O)=O)cnc2C(=O)N1
SMILES OpenEye OEToolkits 2.0.6 c1nc2c(n1CC(COCCP(=O)(O)O)COCP(=O)(O)O)N=C(NC2=O)N
Canonical SMILES CACTVS 3.385 NC1=Nc2n(C[C@H](COCC[P](O)(O)=O)COC[P](O)(O)=O)cnc2C(=O)N1
Canonical SMILES OpenEye OEToolkits 2.0.6 c1nc2c(n1C[C@H](COCCP(=O)(O)O)COCP(=O)(O)O)N=C(NC2=O)N

IUPAC InChI

InChI=1S/C12H21N5O9P2/c13-12-15-10-9(11(18)16-12)14-6-17(10)3-8(5-26-7-28(22,23)24)4-25-1-2-27(19,20)21/h6,8H,1-5,7H2,(H2,19,20,21)(H2,22,23,24)(H3,13,15,16,18)/t8-/m1/s1

IUPAC InChI key

VTOAZXSSULBZBZ-MRVPVSSYSA-N
9YP

wwPDB Information

Atom count

49 (28 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-06-27

Last modified at

2017-08-25

Status

Released

Obsoleted

Not Assigned



9YP : Atoms of Molecule

Total Number of Atoms: 49
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OAE O O1 N N N 0 6.372 -2.297 -1.409
2 PBA P P1 N N N 0 5.412 -2.134 -0.127
3 OAF O O2 N N N 0 5.213 -3.454 0.512
4 OAC O O3 N N N 0 6.092 -1.125 0.928
5 CAL C C1 N N N 0 3.8 -1.466 -0.655
6 CAK C C2 N N N 0 2.847 -1.428 0.54
7 OAS O O4 N N N 0 1.584 -0.904 0.126
8 CAM C C3 N N N 0 0.615 -0.825 1.174
9 CAY C C4 R N N 0 -0.691 -0.254 0.619
10 CAN C C5 N N N 0 -0.465 1.191 0.168
11 OAT O O5 N N N 0 0.451 1.209 -0.928
12 CAO C C6 N N N 0 0.733 2.518 -1.429
13 PBB P P2 N N N 0 1.848 3.383 -0.274
14 OAG O O6 N N N 0 2.165 4.857 -0.838
15 OAH O O7 N N N 0 1.198 3.49 1.051
16 OAD O O8 N N N 0 3.221 2.555 -0.133
17 CAP C C7 N N N 0 -1.765 -0.286 1.708
18 NAZ N N1 N Y N 0 -3.046 0.149 1.144
19 CAW C C8 N Y N 0 -3.948 -0.638 0.483
20 CAJ N N2 N N N 0 -3.988 -1.934 0.151
21 CAU C C9 N N N 0 -5.011 -2.436 -0.504
22 NAA N N3 N N N 0 -5.008 -3.771 -0.823
23 NAR N N4 N N N 0 -6.076 -1.67 -0.875
24 CAV C C10 N N N 0 -6.106 -0.352 -0.574
25 OAB O O9 N N N 0 -7.053 0.342 -0.901
26 CAX C C11 N Y N 0 -5.011 0.201 0.13
27 NAQ N N5 N Y N 0 -4.711 1.442 0.585
28 CAI C C12 N Y N 0 -3.559 1.413 1.188
29 H1 H H1 N N N 0 7.248 -2.649 -1.202
30 H2 H H2 N N N 0 6.252 -0.238 0.576
31 H3 H H3 N N N 0 3.935 -0.457 -1.045
32 H4 H H4 N N N 0 3.381 -2.103 -1.434
33 H5 H H5 N N N 0 2.712 -2.437 0.93
34 H6 H H6 N N N 0 3.266 -0.791 1.319
35 H7 H H7 N N N 0 0.434 -1.822 1.576
36 H8 H H8 N N N 0 0.988 -0.176 1.966
37 H9 H H9 N N N 0 -1.018 -0.853 -0.231
38 H10 H H10 N N N 0 -1.414 1.627 -0.145
39 H11 H H11 N N N 0 -0.054 1.769 0.995
40 H12 H H12 N N N 0 1.211 2.439 -2.405
41 H13 H H13 N N N 0 -0.197 3.078 -1.524
42 H14 H H14 N N N 0 2.754 5.376 -0.273
43 H15 H H15 N N N 0 3.702 2.445 -0.965
44 H16 H H16 N N N 0 -1.863 -1.301 2.092
45 H17 H H17 N N N 0 -1.48 0.384 2.52
46 H18 H H18 N N N 0 -4.258 -4.329 -0.565
47 H19 H H19 N N N 0 -5.756 -4.156 -1.306
48 H20 H H20 N N N 0 -6.815 -2.072 -1.357
49 H21 H H21 N N N 0 -3.076 2.264 1.646



9YP : Chemical Bonds

Total Number of Bonds: 50
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OAB CAV O C doub 1.22 N N
2 OAH PBB O P doub 1.48 N N
3 NAQ CAI N C doub 1.3 N Y
4 NAQ CAX N C sing 1.36 N Y
5 OAD PBB O P sing 1.61 N N
6 CAV CAX C C sing 1.41 N N
7 CAV NAR C N sing 1.35 N N
8 PBB CAO P C sing 1.82 N N
9 PBB OAG P O sing 1.61 N N
10 CAI NAZ C N sing 1.36 N Y
11 CAX CAW C C doub 1.4 N Y
12 CAO OAT C O sing 1.43 N N
13 NAR CAU N C sing 1.36 N N
14 NAZ CAW N C sing 1.37 N Y
15 NAZ CAP N C sing 1.47 N N
16 CAW CAJ C N sing 1.34 N N
17 CAN OAT C O sing 1.43 N N
18 CAN CAY C C sing 1.53 N N
19 CAU CAJ C N doub 1.31 N N
20 CAU NAA C N sing 1.37 N N
21 CAP CAY C C sing 1.53 N N
22 CAY CAM C C sing 1.53 N N
23 CAM OAS C O sing 1.43 N N
24 OAS CAK O C sing 1.43 N N
25 CAK CAL C C sing 1.53 N N
26 OAF PBA O P doub 1.48 N N
27 CAL PBA C P sing 1.82 N N
28 OAE PBA O P sing 1.61 N N
29 PBA OAC P O sing 1.61 N N
30 OAE H1 O H sing 0.97 N N
31 OAC H2 O H sing 0.97 N N
32 CAL H3 C H sing 1.09 N N
33 CAL H4 C H sing 1.09 N N
34 CAK H5 C H sing 1.09 N N
35 CAK H6 C H sing 1.09 N N
36 CAM H7 C H sing 1.09 N N
37 CAM H8 C H sing 1.09 N N
38 CAY H9 C H sing 1.09 N N
39 CAN H10 C H sing 1.09 N N
40 CAN H11 C H sing 1.09 N N
41 CAO H12 C H sing 1.09 N N
42 CAO H13 C H sing 1.09 N N
43 OAG H14 O H sing 0.97 N N
44 OAD H15 O H sing 0.97 N N
45 CAP H16 C H sing 1.09 N N
46 CAP H17 C H sing 1.09 N N
47 NAA H18 N H sing 0.97 N N
48 NAA H19 N H sing 0.97 N N
49 NAR H20 N H sing 0.97 N N
50 CAI H21 C H sing 1.08 N N



9YP : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
9YP 5w8v Open in New Window Bound ligand 4 1