Chemical Components in the PDB

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C2F : Summary

Code

C2F

One-letter code

X

Molecule name

5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID

Systematic names

ProgramVersionName
ACDLabs 10.04 N-{[4-({[(6S)-2-amino-5-methyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid
OpenEye OEToolkits 1.5.0 (2S)-2-[[4-[[(5R,6S)-2-amino-5-methyl-4-oxo-3,6,7,8-tetrahydropteridin-6-yl]methylamino]phenyl]carbonylamino]pentanedioic acid

Formula

C20 H25 N7 O6

Formal charge

0

Molecular weight

459.456 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C(NC(=O)c1ccc(cc1)NCC2N(C=3C(=O)NC(=NC=3NC2)N)C)CCC(=O)O
SMILES CACTVS 3.341 CN1[CH](CNc2ccc(cc2)C(=O)N[CH](CCC(O)=O)C(O)=O)CNC3=C1C(=O)NC(=N3)N
SMILES OpenEye OEToolkits 1.5.0 CN1C(CNC2=C1C(=O)NC(=N2)N)CNc3ccc(cc3)C(=O)NC(CCC(=O)O)C(=O)O
Canonical SMILES CACTVS 3.341 CN1[C@@H](CNc2ccc(cc2)C(=O)N[C@@H](CCC(O)=O)C(O)=O)CNC3=C1C(=O)NC(=N3)N
Canonical SMILES OpenEye OEToolkits 1.5.0 C[N@@]1[C@H](CNC2=C1C(=O)NC(=N2)N)CNc3ccc(cc3)C(=O)N[C@@H](CCC(=O)O)C(=O)O

IUPAC InChI

InChI=1S/C20H25N7O6/c1-27-12(9-23-16-15(27)18(31)26-20(21)25-16)8-22-11-4-2-10(3-5-11)17(30)24-13(19(32)33)6-7-14(28)29/h2-5,12-13,22H,6-9H2,1H3,(H,24,30)(H,28,29)(H,32,33)(H4,21,23,25,26,31)/t12-,13-/m0/s1

IUPAC InChI key

ZNOVTXRBGFNYRX-STQMWFEESA-N
C2F

wwPDB Information

Atom count

58 (33 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



C2F : Atoms of Molecule

Total Number of Atoms: 58
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N Y N 0 2.193 -0.89 5.344
2 C2 C C2 N Y N 0 2.696 0.29 5.636
3 NA2 N NA2 N N N 0 4.036 0.397 5.911
4 N3 N N3 N Y N 0 1.921 1.408 5.666
5 C4 C C4 N Y N 0 0.599 1.326 5.401
6 O4 O O4 N N N 0 -0.106 2.323 5.427
7 C4A C C4A N Y N 0 0.057 0.073 5.095
8 N5 N N5 N N N 0 -1.32 -0.072 4.821
9 C6 C C6 S N N 0 -1.778 -1.309 4.168
10 C7 C C7 N N N 0 -1.08 -2.494 4.852
11 N8 N N8 N N N 0 0.372 -2.285 4.77
12 C8A C C8A N Y N 0 0.891 -1.037 5.075
13 C9 C C9 N N N 0 -1.41 -1.277 2.684
14 N10 N N10 N N N 0 -2.053 -0.125 2.046
15 C11 C C11 N N N 0 -2.27 0.985 5.173
16 C12 C C12 N Y N 0 -1.486 0.588 -2.014
17 C13 C C13 N Y N 0 -2.289 1.447 -1.257
18 C14 C C14 N Y N 0 -2.475 1.208 0.085
19 C15 C C15 N Y N 0 -1.863 0.113 0.689
20 C16 C C16 N Y N 0 -1.058 -0.74 -0.06
21 C17 C C17 N Y N 0 -0.874 -0.509 -1.404
22 C C C N N N 0 -1.286 0.841 -3.453
23 O O O N N N 0 -1.819 1.797 -3.983
24 N N N N N N 0 -0.511 0.013 -4.181
25 CA C CA S N N 0 -0.312 0.264 -5.611
26 CB C CB N N N 0 1.064 -0.252 -6.033
27 CG C CG N N N 0 2.148 0.472 -5.232
28 CD C CD N N N 0 3.504 -0.036 -5.647
29 OE1 O OE1 N N N 0 3.594 -0.891 -6.497
30 OE2 O OE2 N N N 0 4.612 0.459 -5.074
31 CT C CT N N N 0 -1.38 -0.448 -6.4
32 O1 O O1 N N N 0 -1.756 0.0040 -7.454
33 O2 O O2 N N N 0 -1.912 -1.588 -5.931
34 HN21 H 1HN2 N N N 0 4.599 -0.392 5.893
35 HN22 H 2HN2 N N N 0 4.42 1.261 6.124
36 HN3 H HN3 N N N 0 2.319 2.267 5.879
37 H6 H H6 N N N 0 -2.859 -1.405 4.278
38 H71 H 1H7 N N N 0 -1.385 -2.547 5.897
39 H72 H 2H7 N N N 0 -1.347 -3.42 4.343
40 HN8 H HN8 N N N 0 0.959 -3.011 4.507
41 H91 H 1H9 N N N 0 -0.328 -1.193 2.579
42 H92 H 2H9 N N N 0 -1.751 -2.195 2.205
43 HN1 H HN1 N N N 0 -2.61 0.47 2.57
44 H111 H 1H11 N N N 0 -2.056 1.877 4.585
45 H112 H 2H11 N N N 0 -3.285 0.646 4.963
46 H113 H 3H11 N N N 0 -2.178 1.219 6.234
47 H13 H H13 N N N 0 -2.764 2.296 -1.725
48 H14 H H14 N N N 0 -3.095 1.87 0.67
49 H16 H H16 N N N 0 -0.585 -1.588 0.411
50 H17 H H17 N N N 0 -0.253 -1.174 -1.986
51 HN H HN N N N 0 -0.085 -0.749 -3.759
52 HA H HA N N N 0 -0.373 1.335 -5.804
53 HB1 H 1HB N N N 0 1.125 -1.323 -5.84
54 HB2 H 2HB N N N 0 1.212 -0.065 -7.096
55 HG1 H 1HG N N N 0 2.087 1.543 -5.425
56 HG2 H 2HG N N N 0 2.0 0.285 -4.168
57 HOE2 H 2HOE N N N 0 5.482 0.132 -5.34
58 HO2 H HO2 N N N 0 -2.597 -2.046 -6.437



C2F : Chemical Bonds

Total Number of Bonds: 60
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C2 N C doub 1.32 N Y
2 N1 C8A N C sing 1.34 N Y
3 C2 NA2 C N sing 1.37 N N
4 C2 N3 C N sing 1.36 N Y
5 NA2 HN21 N H sing 0.97 N N
6 NA2 HN22 N H sing 0.97 N N
7 N3 C4 N C sing 1.35 N Y
8 N3 HN3 N H sing 0.97 N N
9 C4 O4 C O doub 1.22 N N
10 C4 C4A C C sing 1.4 N Y
11 C4A N5 C N sing 1.41 N N
12 C4A C8A C C doub 1.39 N Y
13 N5 C6 N C sing 1.47 N N
14 N5 C11 N C sing 1.46 N N
15 C6 C7 C C sing 1.54 N N
16 C6 C9 C C sing 1.53 N N
17 C6 H6 C H sing 1.09 N N
18 C7 N8 C N sing 1.47 N N
19 C7 H71 C H sing 1.09 N N
20 C7 H72 C H sing 1.09 N N
21 N8 C8A N C sing 1.39 N N
22 N8 HN8 N H sing 0.97 N N
23 C9 N10 C N sing 1.47 N N
24 C9 H91 C H sing 1.09 N N
25 C9 H92 C H sing 1.09 N N
26 N10 C15 N C sing 1.39 N N
27 N10 HN1 N H sing 0.97 N N
28 C11 H111 C H sing 1.09 N N
29 C11 H112 C H sing 1.09 N N
30 C11 H113 C H sing 1.09 N N
31 C12 C13 C C doub 1.4 N Y
32 C12 C17 C C sing 1.4 N Y
33 C12 C C C sing 1.47 N N
34 C13 C14 C C sing 1.38 N Y
35 C13 H13 C H sing 1.08 N N
36 C14 C15 C C doub 1.39 N Y
37 C14 H14 C H sing 1.08 N N
38 C15 C16 C C sing 1.39 N Y
39 C16 C17 C C doub 1.38 N Y
40 C16 H16 C H sing 1.08 N N
41 C17 H17 C H sing 1.08 N N
42 C O C O doub 1.22 N N
43 C N C N sing 1.35 N N
44 N CA N C sing 1.47 N N
45 N HN N H sing 0.97 N N
46 CA CB C C sing 1.53 N N
47 CA CT C C sing 1.51 N N
48 CA HA C H sing 1.09 N N
49 CB CG C C sing 1.53 N N
50 CB HB1 C H sing 1.09 N N
51 CB HB2 C H sing 1.09 N N
52 CG CD C C sing 1.51 N N
53 CG HG1 C H sing 1.09 N N
54 CG HG2 C H sing 1.09 N N
55 CD OE1 C O doub 1.21 N N
56 CD OE2 C O sing 1.34 N N
57 OE2 HOE2 O H sing 0.97 N N
58 CT O1 C O doub 1.21 N N
59 CT O2 C O sing 1.34 N N
60 O2 HO2 O H sing 0.97 N N



C2F : Used in PDB Entries

Total Number of PDB Entries: 25
Ligand Code PDB Entry ID Type Total Distinct
C2F 1b02 Open in New Window Bound ligand 1 1
C2F 1q8j Open in New Window Bound ligand 2 1
C2F 1tls Open in New Window Bound ligand 2 1
C2F 1tsn Open in New Window Bound ligand 1 1
C2F 1u1j Open in New Window Bound ligand 1 1
C2F 1xpg Open in New Window Bound ligand 2 1
C2F 1xr2 Open in New Window Bound ligand 2 1
C2F 1zp4 Open in New Window Bound ligand 3 1
C2F 2e7f Open in New Window Bound ligand 2 1
C2F 2idk Open in New Window Bound ligand 2 1
C2F 2ogy Open in New Window Bound ligand 2 1
C2F 2ycj Open in New Window Bound ligand 1 1
C2F 3a8i Open in New Window Bound ligand 4 1
C2F 3fsu Open in New Window Bound ligand 2 1
C2F 3ijd Open in New Window Bound ligand 4 1
C2F 3thr Open in New Window Bound ligand 4 1
C2F 4dje Open in New Window Bound ligand 2 1
C2F 4djf Open in New Window Bound ligand 2 1
C2F 4fog Open in New Window Bound ligand 3 1
C2F 4l64 Open in New Window Bound ligand 1 1
C2F 4l65 Open in New Window Bound ligand 1 1
C2F 4o1e Open in New Window Bound ligand 2 1
C2F 5fct Open in New Window Bound ligand 2 1
C2F 5voo Open in New Window Bound ligand 6 1
C2F 5vop Open in New Window Bound ligand 2 1