Chemical Components in the PDB

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G7M : Summary

Code

G7M

One-letter code

G

Molecule name

N7-METHYL-GUANOSINE-5'-MONOPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 7-methylguanosine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 1.5.0 [(2R,3S,4R,5R)-5-(2-amino-7-methyl-6-oxo-1H-purin-7-ium-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C11 H17 N5 O8 P

Formal charge

1

Molecular weight

378.255 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1c2[n+](cn(c2N=C(N)N1)C3OC(C(O)C3O)COP(=O)(O)O)C
SMILES CACTVS 3.341 C[n+]1cn([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)c3N=C(N)NC(=O)c13
SMILES OpenEye OEToolkits 1.5.0 C[n+]1cn(c2c1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(O)O)O)O
Canonical SMILES CACTVS 3.341 C[n+]1cn([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)c3N=C(N)NC(=O)c13
Canonical SMILES OpenEye OEToolkits 1.5.0 C[n+]1cn(c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O

IUPAC InChI

InChI=1S/C11H16N5O8P/c1-15-3-16(8-5(15)9(19)14-11(12)13-8)10-7(18)6(17)4(24-10)2-23-25(20,21)22/h3-4,6-7,10,17-18H,2H2,1H3,(H4-,12,13,14,19,20,21,22)/p+1/t4-,6-,7-,10-/m1/s1

IUPAC InChI key

AOKQNZVJJXPUQA-KQYNXXCUSA-O
G7M

wwPDB Information

Atom count

42 (25 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

G

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



G7M : Atoms of Molecule

Total Number of Atoms: 42
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1' C C1* R N N 0 -0.374 -0.819 0.26
2 C2 C C2 N N N 0 -4.812 -0.891 0.859
3 C2' C C2* R N N 0 -0.217 -1.769 -0.947
4 C3' C C3* S N N 0 1.308 -2.015 -1.033
5 C4 C C4 N Y N 0 -2.768 -0.0070 0.242
6 C4' C C4* R N N 0 1.888 -1.187 0.135
7 C5 C C5 N Y N 0 -3.387 1.185 -0.15
8 C5' C C5* N N N 0 3.225 -0.559 -0.266
9 C6 C C6 N N N 0 -4.791 1.294 -0.019
10 C8 C C8 N Y N 0 -1.264 1.412 -0.519
11 CN7 C CN7 N N N 0 -2.628 3.365 -1.125
12 H1 H H1 N N N 0 -6.435 0.296 0.593
13 H1' H H1* N N N 0 -0.596 -1.387 1.164
14 H2' H H2* N N N 0 -0.578 -1.291 -1.858
15 H21 H 1H2 N N N 0 -5.073 -2.755 1.64
16 H22 H 2H2 N N N 0 -6.492 -1.871 1.468
17 H3' H H3* N N N 0 1.701 -1.659 -1.985
18 H4' H H4* N N N 0 2.014 -1.813 1.018
19 H5' H 1H5* N N N 0 3.921 -1.344 -0.56
20 H5'' H 2H5* N N N 0 3.07 0.122 -1.104
21 H8 H H8 N N N 0 -0.317 1.84 -0.812
22 HN71 H 1HN7 N N N 0 -2.802 3.322 -2.2
23 HN72 H 2HN7 N N N 0 -3.494 3.809 -0.634
24 HN73 H 3HN7 N N N 0 -1.745 3.972 -0.924
25 HO2' H 2HO* N N N 0 -0.723 -3.568 -1.478
26 HO3' H H3T N N Y 0 1.218 -3.867 -1.613
27 HOP2 H 2HOP N N N 0 6.72 1.881 1.257
28 HOP3 H 3HOP N N N 0
29 N1 N N1 N N N 0 -5.472 0.243 0.49
30 N2 N N2 N N N 0 -5.529 -1.942 1.373
31 N3 N N3 N N N 0 -3.508 -1.006 0.738
32 N7 N N7 N Y N 1 -2.415 2.01 -0.611
33 N9 N N9 N Y N 0 -1.432 0.162 0.0030
34 O2' O O2* N N N 0 -0.91 -2.998 -0.72
35 O3' O O3* N N N 0 1.603 -3.402 -0.858
36 O4' O O4* N N N 0 0.904 -0.159 0.383
37 O5' O O5* N N N 0 3.763 0.165 0.842
38 O6 O O6 N N N 0 -5.373 2.313 -0.352
39 OP1 O O1P N N N 0 4.884 1.875 -0.811
40 OP2 O O2P N N N 0 5.889 1.518 1.593
41 OP3 O O3P N N Y 0 6.031 -0.281 -0.172
42 P P P N N N 0 5.161 0.795 0.352



G7M : Chemical Bonds

Total Number of Bonds: 44
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OP3 P O P sing 1.48 N N
2 OP3 HOP3 O H sing N N
3 P OP1 P O doub 1.61 N N
4 P OP2 P O sing 1.61 N N
5 P O5' P O sing 1.61 N N
6 OP2 HOP2 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' C H sing 1.09 N N
10 C5' H5'' 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 CN7 N C sing 1.46 N N
30 N7 C5 N C sing 1.36 N Y
31 CN7 HN71 C H sing 1.09 N N
32 CN7 HN72 C H sing 1.09 N N
33 CN7 HN73 C H sing 1.09 N N
34 C5 C6 C C sing 1.41 N N
35 C5 C4 C C doub 1.4 N Y
36 C6 O6 C O doub 1.22 N N
37 C6 N1 C N sing 1.35 N N
38 N1 C2 N C sing 1.36 N N
39 N1 H1 N H sing 0.97 N N
40 C2 N2 C N sing 1.37 N N
41 C2 N3 C N doub 1.31 N N
42 N2 H21 N H sing 0.97 N N
43 N2 H22 N H sing 0.97 N N
44 N3 C4 N C sing 1.34 N N



G7M : Used in PDB Entries

Total Number of PDB Entries: 168
Ligand Code PDB Entry ID Type Total Distinct
G7M 1c0a Open in New Window Polymer component 1 1
G7M 1efw Open in New Window Polymer component 2 1
G7M 1n1h Open in New Window Bound ligand 1 1
G7M 1qf6 Open in New Window Polymer component 1 1
G7M 1xmm Open in New Window Bound ligand 2 1
G7M 4ybb Open in New Window Polymer component 4 3
G7M 4zer Open in New Window Polymer component 2 1
G7M 5br8 Open in New Window Polymer component 1 1
G7M 5e7k Open in New Window Polymer component 2 1
G7M 5e81 Open in New Window Polymer component 2 1
G7M 5el5 Open in New Window Polymer component 2 1
G7M 5el6 Open in New Window Polymer component 2 1
G7M 5el7 Open in New Window Polymer component 2 1
G7M 5fdv Open in New Window Polymer component 2 1
G7M 5iqr Open in New Window Polymer component 2 2
G7M 5it8 Open in New Window Polymer component 4 3
G7M 5j5b Open in New Window Polymer component 4 3
G7M 5j7l Open in New Window Polymer component 4 3
G7M 5j91 Open in New Window Polymer component 4 3
G7M 5jc9 Open in New Window Polymer component 4 3
G7M 5kcr Open in New Window Polymer component 1 1
G7M 5kcs Open in New Window Polymer component 1 1
G7M 5lmq Open in New Window Polymer component 1 1
G7M 5lmr Open in New Window Polymer component 1 1
G7M 5lms Open in New Window Polymer component 1 1
G7M 5lmt Open in New Window Polymer component 1 1
G7M 5lmu Open in New Window Polymer component 1 1
G7M 5lmv Open in New Window Polymer component 1 1
G7M 5lza Open in New Window Polymer component 2 2
G7M 5lzb Open in New Window Polymer component 2 2
G7M 5lzc Open in New Window Polymer component 2 2
G7M 5lzd Open in New Window Polymer component 2 2
G7M 5lze Open in New Window Polymer component 2 2
G7M 5lzf Open in New Window Polymer component 2 2
G7M 5mdv Open in New Window Polymer component 1 1
G7M 5mdw Open in New Window Polymer component 1 1
G7M 5mdy Open in New Window Polymer component 1 1
G7M 5mdz Open in New Window Polymer component 1 1
G7M 5me0 Open in New Window Polymer component 1 1
G7M 5me1 Open in New Window Polymer component 1 1
G7M 5no2 Open in New Window Polymer component 1 1
G7M 5no3 Open in New Window Polymer component 1 1
G7M 5no4 Open in New Window Polymer component 1 1
G7M 5u4j Open in New Window Polymer component 2 2
G7M 5v8i Open in New Window Polymer component 2 1
G7M 5w4k Open in New Window Polymer component 6 4
G7M 6c4h Open in New Window Polymer component 1 1
G7M 6c4i Open in New Window Polymer component 2 2
G7M 6cao Open in New Window Polymer component 1 1
G7M 6cap Open in New Window Polymer component 1 1
G7M 6caq Open in New Window Polymer component 1 1
G7M 6car Open in New Window Polymer component 1 1
G7M 6cas Open in New Window Polymer component 1 1
G7M 6czr Open in New Window Polymer component 2 1
G7M 6hrm Open in New Window Polymer component 1 1
G7M 6i7v Open in New Window Polymer component 2 2
G7M 6n1d Open in New Window Polymer component 2 1
G7M 6ndk Open in New Window Polymer component 2 1
G7M 6om6 Open in New Window Polymer component 1 1
G7M 6ord Open in New Window Polymer component 2 1
G7M 6ore Open in New Window Polymer component 2 2
G7M 6orl Open in New Window Polymer component 1 1
G7M 6osk Open in New Window Polymer component 2 2
G7M 6osq Open in New Window Polymer component 2 2
G7M 6ost Open in New Window Polymer component 2 2
G7M 6ot3 Open in New Window Polymer component 2 2
G7M 6ouo Open in New Window Polymer component 2 2
G7M 6pc5 Open in New Window Polymer component 1 1
G7M 6pc6 Open in New Window Polymer component 1 1
G7M 6pc7 Open in New Window Polymer component 1 1
G7M 6pc8 Open in New Window Polymer component 1 1
G7M 6pch Open in New Window Polymer component 1 1
G7M 6pcq Open in New Window Polymer component 1 1
G7M 6pcr Open in New Window Polymer component 1 1
G7M 6pcs Open in New Window Polymer component 1 1
G7M 6pct Open in New Window Polymer component 1 1
G7M 6pj6 Open in New Window Polymer component 1 1
G7M 6q97 Open in New Window Polymer component 1 1
G7M 6q98 Open in New Window Polymer component 1 1
G7M 6q9a Open in New Window Polymer component 1 1
G7M 6tbv Open in New Window Polymer component 3 3
G7M 6tc3 Open in New Window Polymer component 3 3
G7M 6tnu Open in New Window Polymer component 1 1
G7M 6u48 Open in New Window Polymer component 1 1
G7M 6vz3 Open in New Window Polymer component 1 1
G7M 6vz7 Open in New Window Polymer component 1 1
G7M 6wyv Open in New Window Polymer component 1 1
G7M 6xa1 Open in New Window Polymer component 2 2
G7M 6xz7 Open in New Window Polymer component 1 1
G7M 6xza Open in New Window Polymer component 2 2
G7M 6xzb Open in New Window Polymer component 2 2
G7M 6ysr Open in New Window Polymer component 3 3
G7M 6yss Open in New Window Polymer component 3 3
G7M 6yst Open in New Window Polymer component 3 3
G7M 6ysu Open in New Window Polymer component 3 3
G7M 6ztj Open in New Window Polymer component 2 2
G7M 6ztl Open in New Window Polymer component 2 2
G7M 6ztm Open in New Window Polymer component 2 2
G7M 6ztn Open in New Window Polymer component 2 2
G7M 6zto Open in New Window Polymer component 2 2
G7M 6ztp Open in New Window Polymer component 2 2
G7M 6zu1 Open in New Window Polymer component 3 3
G7M 6zu9 Open in New Window Polymer component 1 1
G7M 7abz Open in New Window Polymer component 3 3
G7M 7ac7 Open in New Window Polymer component 3 3
G7M 7acj Open in New Window Polymer component 2 2
G7M 7acr Open in New Window Polymer component 2 2
G7M 7af3 Open in New Window Polymer component 1 1
G7M 7af5 Open in New Window Polymer component 1 1
G7M 7af8 Open in New Window Polymer component 1 1
G7M 7afa Open in New Window Polymer component 1 1
G7M 7afd Open in New Window Polymer component 1 1
G7M 7afh Open in New Window Polymer component 1 1
G7M 7afi Open in New Window Polymer component 1 1
G7M 7afk Open in New Window Polymer component 1 1
G7M 7afl Open in New Window Polymer component 1 1
G7M 7afn Open in New Window Polymer component 1 1
G7M 7b5k Open in New Window Polymer component 2 2
G7M 7bod Open in New Window Polymer component 1 1
G7M 7boe Open in New Window Polymer component 1 1
G7M 7bof Open in New Window Polymer component 1 1
G7M 7bog Open in New Window Polymer component 1 1
G7M 7boh Open in New Window Polymer component 1 1
G7M 7boi Open in New Window Polymer component 1 1
G7M 7cpj Open in New Window Polymer component 3 3
G7M 7k00 Open in New Window Polymer component 2 2
G7M 7kgb Open in New Window Polymer component 1 1
G7M 7ls1 Open in New Window Polymer component 3 3
G7M 7ls2 Open in New Window Polymer component 3 3
G7M 7lvk Open in New Window Polymer component 1 1
G7M 7m4w Open in New Window Polymer component 2 2
G7M 7m4x Open in New Window Polymer component 2 2
G7M 7n1p Open in New Window Polymer component 3 3
G7M 7n2c Open in New Window Polymer component 3 3
G7M 7n2u Open in New Window Polymer component 4 4
G7M 7n30 Open in New Window Polymer component 4 4
G7M 7nar Open in New Window Polymer component 1 1
G7M 7nas Open in New Window Polymer component 1 1
G7M 7nat Open in New Window Polymer component 1 1
G7M 7nau Open in New Window Polymer component 1 1
G7M 7nav Open in New Window Polymer component 1 1
G7M 7nax Open in New Window Polymer component 1 1
G7M 7nwt Open in New Window Polymer component 1 1
G7M 7nww Open in New Window Polymer component 2 2
G7M 7o19 Open in New Window Polymer component 2 2
G7M 7o1a Open in New Window Polymer component 3 3
G7M 7o1c Open in New Window Polymer component 2 2
G7M 7o7z Open in New Window Polymer component 2 2
G7M 7o80 Open in New Window Polymer component 1 1
G7M 7o81 Open in New Window Polymer component 1 1
G7M 7oif Open in New Window Polymer component 2 2
G7M 7oig Open in New Window Polymer component 2 2
G7M 7oii Open in New Window Polymer component 2 2
G7M 7oiz Open in New Window Polymer component 1 1
G7M 7oj0 Open in New Window Polymer component 2 2
G7M 7ot5 Open in New Window Polymer component 2 2
G7M 7p3k Open in New Window Polymer component 1 1
G7M 7pjs Open in New Window Polymer component 3 3
G7M 7pjt Open in New Window Polymer component 3 3
G7M 7pju Open in New Window Polymer component 3 3
G7M 7pjv Open in New Window Polymer component 3 3
G7M 7pjw Open in New Window Polymer component 3 3
G7M 7pjx Open in New Window Polymer component 3 3
G7M 7pjy Open in New Window Polymer component 3 3
G7M 7pjz Open in New Window Polymer component 3 3
G7M 7s1g Open in New Window Polymer component 1 1
G7M 7s1h Open in New Window Polymer component 1 1
G7M 7s1k Open in New Window Polymer component 1 1