Chemical Components in the PDB

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1YJ : Summary

Code

1YJ

One-letter code

X

Molecule name

N-[4-({[(6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 N-[4-({[(6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid
OpenEye OEToolkits 1.7.6 (2S)-2-[[4-[[(6R)-2-azanyl-4-oxidanylidene-5,6,7,8-tetrahydro-3H-pteridin-6-yl]methylamino]phenyl]carbonylamino]pentanedioic acid

Formula

C19 H23 N7 O6

Formal charge

0

Molecular weight

445.429 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C(NC(=O)c1ccc(cc1)NCC3NC2=C(N=C(N)NC2=O)NC3)CCC(=O)O
SMILES CACTVS 3.385 NC1=NC2=C(N[CH](CNc3ccc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O)CN2)C(=O)N1
SMILES OpenEye OEToolkits 1.7.6 c1cc(ccc1C(=O)NC(CCC(=O)O)C(=O)O)NCC2CNC3=C(N2)C(=O)NC(=N3)N
Canonical SMILES CACTVS 3.385 NC1=NC2=C(N[C@H](CNc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)CN2)C(=O)N1
Canonical SMILES OpenEye OEToolkits 1.7.6 c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@@H]2CNC3=C(N2)C(=O)NC(=N3)N

IUPAC InChI

InChI=1S/C19H23N7O6/c20-19-25-15-14(17(30)26-19)23-11(8-22-15)7-21-10-3-1-9(2-4-10)16(29)24-12(18(31)32)5-6-13(27)28/h1-4,11-12,21,23H,5-8H2,(H,24,29)(H,27,28)(H,31,32)(H4,20,22,25,26,30)/t11-,12+/m1/s1

IUPAC InChI key

MSTNYGQPCMXVAQ-NEPJUHHUSA-N
1YJ

wwPDB Information

Atom count

55 (32 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-08-05

Last modified at

2013-08-09

Status

Released

Obsoleted

Not Assigned



1YJ : Atoms of Molecule

Total Number of Atoms: 55
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N3 N N3 N N N 0 5.775 -2.538 -0.203
2 C2 C C2 N N N 0 6.251 -1.979 -1.349
3 N1 N N1 N N N 0 6.257 -0.676 -1.531
4 C8A C C8A N N N 0 5.791 0.153 -0.589
5 C4A C C4A N N N 0 5.297 -0.367 0.599
6 C4 C C4 N N N 0 5.289 -1.754 0.783
7 N8 N N8 N N N 0 5.8 1.524 -0.791
8 C7 C C7 N N N 0 5.656 2.418 0.367
9 C6 C C6 R N N 0 4.509 1.893 1.243
10 N5 N N5 N N N 0 4.808 0.498 1.602
11 C9 C C9 N N N 0 3.195 1.95 0.463
12 N10 N N10 N N N 0 2.127 1.338 1.259
13 C4' C C4' N Y N 0 0.834 1.273 0.754
14 C3' C C3' N Y N 0 0.555 1.785 -0.511
15 C2' C C2' N Y N 0 -0.725 1.722 -1.013
16 C1' C C1' N Y N 0 -1.745 1.144 -0.253
17 C6' C C6' N Y N 0 -1.462 0.632 1.017
18 C5' C C5' N Y N 0 -0.18 0.692 1.511
19 C11 C C11 N N N 0 -3.118 1.076 -0.788
20 N N N N N N 0 -4.101 0.518 -0.054
21 CA C CA S N N 0 -5.464 0.451 -0.586
22 C C C N N N 0 -6.181 1.745 -0.298
23 OX2 O OX2 N N N 0 -7.452 1.911 -0.696
24 OX1 O OX1 N N N 0 -5.611 2.633 0.291
25 CB C CB N N N 0 -6.214 -0.706 0.078
26 CG C CG N N N 0 -5.559 -2.031 -0.316
27 CD C CD N N N 0 -6.298 -3.171 0.338
28 OE1 O OE1 N N N 0 -7.25 -2.945 1.047
29 OE2 O OE2 N N N 0 -5.897 -4.435 0.134
30 O11 O O11 N N N 0 -3.363 1.523 -1.892
31 O4 O O4 N N N 0 4.859 -2.244 1.817
32 N2 N N2 N N N 0 6.738 -2.795 -2.339
33 H3 H H3 N N N 0 6.582 2.427 0.942
34 H4 H H4 N N N 0 5.425 3.427 0.026
35 H5 H H5 N N N 0 4.429 2.498 2.146
36 H6 H H6 N N N 0 4.678 0.181 2.51
37 H8 H H8 N N N 0 2.941 2.989 0.253
38 H9 H H9 N N N 0 1.344 2.232 -1.097
39 H10 H H10 N N N 0 -0.94 2.12 -1.994
40 H11 H H11 N N N 0 -2.249 0.185 1.607
41 H12 H H12 N N N 0 0.041 0.292 2.49
42 H13 H H13 N N N 0 -3.906 0.162 0.827
43 H14 H H14 N N N 0 -5.426 0.288 -1.663
44 H15 H H15 N N N 0 -7.87 2.758 -0.489
45 H16 H H16 N N N 0 -6.175 -0.59 1.161
46 H17 H H17 N N N 0 -7.253 -0.702 -0.251
47 H18 H H18 N N N 0 -5.598 -2.148 -1.399
48 H19 H H19 N N N 0 -4.52 -2.035 0.013
49 H20 H H20 N N N 0 -6.402 -5.132 0.575
50 H21 H H21 N N N 0 6.739 -3.757 -2.218
51 H22 H H22 N N N 0 7.08 -2.409 -3.161
52 H23 H H23 N N N 0 5.781 -3.502 -0.096
53 H1 H H1 N N N 0 5.901 1.889 -1.684
54 H2 H H2 N N N 0 3.305 1.406 -0.475
55 H7 H H7 N N N 0 2.323 0.979 2.138



1YJ : Chemical Bonds

Total Number of Bonds: 57
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C7 N8 C N sing 1.47 N N
2 C7 C6 C C sing 1.54 N N
3 N8 C8A N C sing 1.39 N N
4 C6 N5 C N sing 1.47 N N
5 C6 C9 C C sing 1.53 N N
6 N10 C9 N C sing 1.47 N N
7 N10 C4' N C sing 1.39 N N
8 C3' C4' C C doub 1.39 N Y
9 C3' C2' C C sing 1.38 N Y
10 C8A C4A C C doub 1.39 N N
11 C8A N1 C N sing 1.34 N N
12 N5 C4A N C sing 1.41 N N
13 C4' C5' C C sing 1.39 N Y
14 C4A C4 C C sing 1.4 N N
15 N1 C2 N C doub 1.32 N N
16 C2' C1' C C doub 1.4 N Y
17 C2 N3 C N sing 1.36 N N
18 C2 N2 C N sing 1.37 N N
19 C4 N3 C N sing 1.35 N N
20 C4 O4 C O doub 1.22 N N
21 C5' C6' C C doub 1.38 N Y
22 C1' C6' C C sing 1.4 N Y
23 C1' C11 C C sing 1.48 N N
24 O11 C11 O C doub 1.22 N N
25 C11 N C N sing 1.35 N N
26 N CA N C sing 1.46 N N
27 CA C C C sing 1.51 N N
28 CA CB C C sing 1.53 N N
29 C OX1 C O doub 1.21 N N
30 C OX2 C O sing 1.34 N N
31 CG CB C C sing 1.53 N N
32 CG CD C C sing 1.51 N N
33 OE1 CD O C doub 1.21 N N
34 CD OE2 C O sing 1.34 N N
35 C7 H3 C H sing 1.09 N N
36 C7 H4 C H sing 1.09 N N
37 C6 H5 C H sing 1.09 N N
38 N5 H6 N H sing 0.97 N N
39 C9 H8 C H sing 1.09 N N
40 C3' H9 C H sing 1.08 N N
41 C2' H10 C H sing 1.08 N N
42 C6' H11 C H sing 1.08 N N
43 C5' H12 C H sing 1.08 N N
44 N H13 N H sing 0.97 N N
45 CA H14 C H sing 1.09 N N
46 OX2 H15 O H sing 0.97 N N
47 CB H16 C H sing 1.09 N N
48 CB H17 C H sing 1.09 N N
49 CG H18 C H sing 1.09 N N
50 CG H19 C H sing 1.09 N N
51 OE2 H20 O H sing 0.97 N N
52 N2 H21 N H sing 0.97 N N
53 N2 H22 N H sing 0.97 N N
54 N3 H23 N H sing 0.97 N N
55 N8 H1 N H sing 0.97 N N
56 C9 H2 C H sing 1.09 N N
57 N10 H7 N H sing 0.97 N N



1YJ : Used in PDB Entries

Total Number of PDB Entries: 5
Ligand Code PDB Entry ID Type Total Distinct
1YJ 4ly3 Open in New Window Bound ligand 2 1
1YJ 4yfy Open in New Window Bound ligand 2 1
1YJ 5uil Open in New Window Bound ligand 2 1
1YJ 5vys Open in New Window Bound ligand 2 1
1YJ 6ci5 Open in New Window Bound ligand 1 1