Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

5GP : Summary

Code

5GP

One-letter code

X

Molecule name

GUANOSINE-5'-MONOPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 5'-guanylic acid
OpenEye OEToolkits 1.5.0 [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C10 H14 N5 O8 P

Formal charge

0

Molecular weight

363.221 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3O)COP(=O)(O)O
SMILES CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
SMILES OpenEye OEToolkits 1.5.0 c1nc2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
Canonical SMILES CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N

IUPAC InChI

InChI=1S/C10H14N5O8P/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(23-9)1-22-24(19,20)21/h2-3,5-6,9,16-17H,1H2,(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1

IUPAC InChI key

RQFCJASXJCIDSX-UUOKFMHZSA-N
5GP

wwPDB Information

Atom count

38 (24 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



5GP : Atoms of Molecule

Total Number of Atoms: 38
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 P P P N N N 0 5.076 -0.808 -0.277
2 O1P O O1P N N N 0 5.916 0.337 0.139
3 O2P O O2P N N Y 0 4.843 -1.787 0.98
4 O3P O O3P N N N 0 5.815 -1.615 -1.457
5 O5' O O5* N N N 0 3.655 -0.266 -0.806
6 C5' C C5* N N N 0 3.104 0.537 0.24
7 C4' C C4* R N N 0 1.745 1.086 -0.2
8 O4' O O4* N N N 0 0.792 0.011 -0.345
9 C3' C C3* S N N 0 1.149 1.997 0.896
10 O3' O O3* N N N 0 1.399 3.371 0.596
11 C2' C C2* R N N 0 -0.368 1.698 0.85
12 O2' O O2* N N N 0 -1.101 2.88 0.522
13 C1' C C1* R N N 0 -0.506 0.64 -0.267
14 N9 N N9 N Y N 0 -1.53 -0.346 0.088
15 C8 C C8 N Y N 0 -1.319 -1.538 0.717
16 N7 N N7 N Y N 0 -2.451 -2.16 0.875
17 C5 C C5 N Y N 0 -3.452 -1.407 0.358
18 C6 C C6 N N N 0 -4.853 -1.572 0.249
19 O6 O O6 N N N 0 -5.399 -2.574 0.677
20 N1 N N1 N N N 0 -5.571 -0.589 -0.338
21 C2 C C2 N N N 0 -4.949 0.524 -0.819
22 N2 N N2 N N N 0 -5.703 1.503 -1.415
23 N3 N N3 N N N 0 -3.648 0.689 -0.723
24 C4 C C4 N Y N 0 -2.874 -0.239 -0.15
25 HOP2 H 2HOP N N N 0 4.292 -2.517 0.666
26 HOP3 H 3HOP N N N 0 6.66 -1.922 -1.1
27 H5'1 H 1H5* N N N 0 3.778 1.366 0.455
28 H5'2 H 2H5* N N N 0 2.977 -0.071 1.136
29 H4' H H4* N N N 0 1.844 1.634 -1.137
30 H3' H H3* N N N 0 1.561 1.739 1.872
31 HO3' H *HO3 N N N 0 1.007 3.89 1.311
32 H2' H H2* N N N 0 -0.706 1.292 1.803
33 HO2' H *HO2 N N N 0 -0.926 3.522 1.224
34 H1' H H1* N N N 0 -0.754 1.118 -1.215
35 H8 H H8 N N N 0 -0.356 -1.91 1.037
36 HN1 H HN1 N N N 0 -6.533 -0.68 -0.425
37 HN21 H 1HN2 N N N 0 -5.275 2.303 -1.759
38 HN22 H 2HN2 N N N 0 -6.663 1.394 -1.497



5GP : Chemical Bonds

Total Number of Bonds: 40
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P O1P P O doub 1.48 N N
2 P O2P P O sing 1.61 N N
3 P O3P P O sing 1.61 N N
4 P O5' P O sing 1.61 N N
5 O2P HOP2 O H sing 0.97 N N
6 O3P HOP3 O H sing 0.97 N N
7 O5' C5' O C sing 1.43 N N
8 C5' C4' C C sing 1.53 N N
9 C5' H5'1 C H sing 1.09 N N
10 C5' H5'2 C H sing 1.09 N N
11 C4' O4' C O sing 1.44 N N
12 C4' C3' C C sing 1.54 N N
13 C4' H4' C H sing 1.09 N N
14 O4' C1' O C sing 1.44 N N
15 C3' O3' C O sing 1.43 N N
16 C3' C2' C C sing 1.55 N N
17 C3' H3' C H sing 1.09 N N
18 O3' HO3' O H sing 0.97 N N
19 C2' O2' C O sing 1.43 N N
20 C2' C1' C C sing 1.54 N N
21 C2' H2' C H sing 1.09 N N
22 O2' HO2' O H sing 0.97 N N
23 C1' N9 C N sing 1.47 N N
24 C1' H1' C H sing 1.09 N N
25 N9 C8 N C sing 1.36 N Y
26 N9 C4 N C sing 1.37 N Y
27 C8 N7 C N doub 1.3 N Y
28 C8 H8 C H sing 1.08 N N
29 N7 C5 N C sing 1.36 N Y
30 C5 C6 C C sing 1.41 N N
31 C5 C4 C C doub 1.4 N Y
32 C6 O6 C O doub 1.22 N N
33 C6 N1 C N sing 1.35 N N
34 N1 C2 N C sing 1.36 N N
35 N1 HN1 N H sing 0.97 N N
36 C2 N2 C N sing 1.37 N N
37 C2 N3 C N doub 1.31 N N
38 N2 HN21 N H sing 0.97 N N
39 N2 HN22 N H sing 0.97 N N
40 N3 C4 N C sing 1.34 N N



5GP : Used in PDB Entries

Total Number of PDB Entries: 164
Ligand Code PDB Entry ID Type Total Distinct
5GP 1a97 Open in New Window Bound ligand 2 1
5GP 1ao0 Open in New Window Bound ligand 4 1
5GP 1c9k Open in New Window Bound ligand 3 1
5GP 1ecb Open in New Window Bound ligand 8 1
5GP 1ex7 Open in New Window Bound ligand 1 1
5GP 1g7c Open in New Window Bound ligand 1 1
5GP 1g9t Open in New Window Bound ligand 1 1
5GP 1gky Open in New Window Bound ligand 1 1
5GP 1hgx Open in New Window Bound ligand 1 1
5GP 1hmp Open in New Window Bound ligand 2 1
5GP 1iyb Open in New Window Bound ligand 2 1
5GP 1j1f Open in New Window Bound ligand 1 1
5GP 1j1g Open in New Window Bound ligand 2 1
5GP 1jxm Open in New Window Bound ligand 1 1
5GP 1lvg Open in New Window Bound ligand 1 1
5GP 1me0 Open in New Window Polymer component 1 1
5GP 1me1 Open in New Window Polymer component 1 1
5GP 1pzm Open in New Window Bound ligand 2 1
5GP 1qk3 Open in New Window Bound ligand 4 1
5GP 1rnc Open in New Window Bound ligand 1 1
5GP 1t9s Open in New Window Bound ligand 2 1
5GP 1vcz Open in New Window Bound ligand 2 1
5GP 1waj Open in New Window Bound ligand 1 1
5GP 1xz8 Open in New Window Bound ligand 1 1
5GP 1znx Open in New Window Bound ligand 1 1
5GP 2a1y Open in New Window Bound ligand 1 1
5GP 2a7r Open in New Window Bound ligand 3 1
5GP 2anb Open in New Window Bound ligand 1 1
5GP 2b8w Open in New Window Bound ligand 2 1
5GP 2ble Open in New Window Bound ligand 1 1
5GP 2bwg Open in New Window Bound ligand 4 1
5GP 2cnw Open in New Window Bound ligand 3 1
5GP 2d4h Open in New Window Bound ligand 2 1
5GP 2fxv Open in New Window Bound ligand 2 1
5GP 2j41 Open in New Window Bound ligand 3 1
5GP 2jbh Open in New Window Bound ligand 2 1
5GP 2jky Open in New Window Bound ligand 2 1
5GP 2jkz Open in New Window Bound ligand 4 1
5GP 2klh Open in New Window Bound ligand 2 1
5GP 2ouq Open in New Window Bound ligand 1 1
5GP 2p1d Open in New Window Bound ligand 1 1
5GP 2pnz Open in New Window Bound ligand 1 1
5GP 2qor Open in New Window Bound ligand 1 1
5GP 2vfa Open in New Window Bound ligand 2 1
5GP 2w27 Open in New Window Bound ligand 4 1
5GP 2xbu Open in New Window Bound ligand 2 1
5GP 2xjc Open in New Window Bound ligand 1 1
5GP 3acc Open in New Window Bound ligand 1 1
5GP 3b89 Open in New Window Bound ligand 1 1
5GP 3dy8 Open in New Window Bound ligand 1 1
5GP 3dys Open in New Window Bound ligand 1 1
5GP 3gcm Open in New Window Bound ligand 3 1
5GP 3kb8 Open in New Window Bound ligand 2 1
5GP 3kia Open in New Window Bound ligand 2 1
5GP 3kyf Open in New Window Bound ligand 4 1
5GP 3kyg Open in New Window Bound ligand 8 1
5GP 3lnc Open in New Window Bound ligand 2 1
5GP 3luh Open in New Window Bound ligand 3 1
5GP 3md7 Open in New Window Bound ligand 1 1
5GP 3n1s Open in New Window Bound ligand 8 1
5GP 3n1t Open in New Window Bound ligand 4 1
5GP 3oxk Open in New Window Bound ligand 1 1
5GP 3pen Open in New Window Bound ligand 1 1
5GP 3py6 Open in New Window Bound ligand 1 1
5GP 3rhn Open in New Window Bound ligand 1 1
5GP 3rl3 Open in New Window Bound ligand 1 1
5GP 3rl4 Open in New Window Bound ligand 1 1
5GP 3slq Open in New Window Bound ligand 2 1
5GP 3tr0 Open in New Window Bound ligand 1 1
5GP 3w5w Open in New Window Bound ligand 1 1
5GP 3x02 Open in New Window Bound ligand 5 1
5GP 3x06 Open in New Window Bound ligand 5 1
5GP 3x08 Open in New Window Bound ligand 3 1
5GP 3x0a Open in New Window Bound ligand 5 1
5GP 3x0c Open in New Window Bound ligand 4 1
5GP 3zpg Open in New Window Bound ligand 2 1
5GP 4ac9 Open in New Window Bound ligand 1 1
5GP 4aca Open in New Window Bound ligand 1 1
5GP 4acb Open in New Window Bound ligand 1 1
5GP 4dwq Open in New Window Bound ligand 2 1
5GP 4egu Open in New Window Bound ligand 2 1
5GP 4ff2 Open in New Window Bound ligand 1 1
5GP 4ff3 Open in New Window Bound ligand 1 1
5GP 4ff4 Open in New Window Bound ligand 1 1
5GP 4fwo Open in New Window Bound ligand 1 1
5GP 4g0z Open in New Window Bound ligand 1 1
5GP 4gty Open in New Window Bound ligand 2 1
5GP 4h2w Open in New Window Bound ligand 1 1
5GP 4hiu Open in New Window Bound ligand 1 1
5GP 4it0 Open in New Window Bound ligand 1 1
5GP 4lm9 Open in New Window Bound ligand 1 1
5GP 4me4 Open in New Window Bound ligand 1 1
5GP 4o7z Open in New Window Bound ligand 1 1
5GP 4o84 Open in New Window Bound ligand 2 1
5GP 4ohf Open in New Window Bound ligand 2 1
5GP 4ojx Open in New Window Bound ligand 1 1
5GP 4p86 Open in New Window Bound ligand 6 1
5GP 4peg Open in New Window Bound ligand 5 1
5GP 4q9f Open in New Window Bound ligand 1 1
5GP 4rht Open in New Window Bound ligand 4 1
5GP 4x4n Open in New Window Bound ligand 1 1
5GP 4x4v Open in New Window Bound ligand 3 1
5GP 4xba Open in New Window Bound ligand 1 1
5GP 4z0g Open in New Window Bound ligand 4 1
5GP 4z87 Open in New Window Bound ligand 4 1
5GP 4zfn Open in New Window Bound ligand 2 1
5GP 5dhb Open in New Window Bound ligand 4 1
5GP 5dhc Open in New Window Bound ligand 8 1
5GP 5esx Open in New Window Bound ligand 2 1
5GP 5jv5 Open in New Window Bound ligand 2 1
5GP 5k1d Open in New Window Bound ligand 1 1
5GP 5km1 Open in New Window Bound ligand 1 1
5GP 5o7f Open in New Window Bound ligand 2 1
5GP 5tc3 Open in New Window Bound ligand 2 1
5GP 5x71 Open in New Window Bound ligand 2 1
5GP 5xtk Open in New Window Bound ligand 1 1
5GP 5y61 Open in New Window Bound ligand 1 1
5GP 5y62 Open in New Window Bound ligand 1 1
5GP 6gaw Open in New Window Bound ligand 2 1
5GP 6gb2 Open in New Window Bound ligand 2 1
5GP 6hgs Open in New Window Bound ligand 2 1
5GP 6i0m Open in New Window Bound ligand 2 1
5GP 6j23 Open in New Window Bound ligand 1 1
5GP 6jig Open in New Window Bound ligand 2 1
5GP 6low Open in New Window Bound ligand 1 1
5GP 6mfu Open in New Window Bound ligand 4 1
5GP 6mxc Open in New Window Bound ligand 6 1
5GP 6o3v Open in New Window Bound ligand 3 1
5GP 6o6b Open in New Window Bound ligand 4 1
5GP 6qsk Open in New Window Bound ligand 3 1
5GP 6rfu Open in New Window Bound ligand 2 1
5GP 6wct Open in New Window Bound ligand 4 1
5GP 6ydp Open in New Window Bound ligand 2 1
5GP 6ydw Open in New Window Bound ligand 1 1
5GP 6yk9 Open in New Window Bound ligand 2 1
5GP 6ykb Open in New Window Bound ligand 2 1
5GP 7bf4 Open in New Window Bound ligand 1 1
5GP 7buj Open in New Window Bound ligand 2 1
5GP 7bum Open in New Window Bound ligand 2 1
5GP 7c4c Open in New Window Bound ligand 4 1
5GP 7f4y Open in New Window Bound ligand 2 1
5GP 7k16 Open in New Window Polymer component 1 1
5GP 7lc7 Open in New Window Bound ligand 1 1
5GP 7mpp Open in New Window Bound ligand 16 1
5GP 7mpq Open in New Window Bound ligand 14 1
5GP 7nqh Open in New Window Bound ligand 2 1
5GP 7nql Open in New Window Bound ligand 2 1
5GP 7nsh Open in New Window Bound ligand 2 1
5GP 7nsi Open in New Window Bound ligand 1 1
5GP 7nsj Open in New Window Bound ligand 1 1
5GP 7p3b Open in New Window Bound ligand 2 1
5GP 7r50 Open in New Window Bound ligand 16 1
5GP 7s5e Open in New Window Bound ligand 6 1
5GP 7tnz Open in New Window Polymer component 2 1
5GP 7tql Open in New Window Bound ligand 1 1
5GP 7u5f Open in New Window Bound ligand 4 1
5GP 7v1e Open in New Window Bound ligand 1 1
5GP 7v1g Open in New Window Bound ligand 1 1
5GP 7va2 Open in New Window Bound ligand 1 1
5GP 7xxk Open in New Window Bound ligand 3 1
5GP 8dcg Open in New Window Bound ligand 2 1
5GP 8egl Open in New Window Bound ligand 12 1
5GP 8odo Open in New Window Bound ligand 4 1
5GP 8vr0 Open in New Window Bound ligand 3 1