Chemical Components in the PDB

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LUD : Summary

Code

LUD

One-letter code

X

Molecule name

N-{4-[(6aR)-3-amino-1,9-dioxo-1,2,5,6,6a,7-hexahydroimidazo[1,5-f]pteridin-8(9H)-yl]benzene-1-carbonyl}-L-glutamic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 N-{4-[(6aR)-3-amino-1,9-dioxo-1,2,5,6,6a,7-hexahydroimidazo[1,5-f]pteridin-8(9H)-yl]benzene-1-carbonyl}-L-glutamic acid
OpenEye OEToolkits 2.0.7 (2~{S})-2-[[4-[(6~{a}~{R})-3-azanyl-1,9-bis(oxidanylidene)-5,6,6~{a},7-tetrahydro-2~{H}-imidazo[1,5-f]pteridin-8-yl]phenyl]carbonylamino]pentanedioic acid

Formula

C20 H21 N7 O7

Formal charge

0

Molecular weight

471.423 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 N=4C2=C(N3C(N(c1ccc(cc1)C(NC(C(=O)O)CCC(O)=O)=O)CC3CN2)=O)C(=O)NC=4N
SMILES CACTVS 3.385 NC1=NC2=C(N3[CH](CN2)CN(C3=O)c4ccc(cc4)C(=O)N[CH](CCC(O)=O)C(O)=O)C(=O)N1
SMILES OpenEye OEToolkits 2.0.7 c1cc(ccc1C(=O)NC(CCC(=O)O)C(=O)O)N2CC3CNC4=C(N3C2=O)C(=O)NC(=N4)N
Canonical SMILES CACTVS 3.385 NC1=NC2=C(N3[C@H](CN2)CN(C3=O)c4ccc(cc4)C(=O)N[C@@H](CCC(O)=O)C(O)=O)C(=O)N1
Canonical SMILES OpenEye OEToolkits 2.0.7 c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)N2C[C@H]3CNC4=C(N3C2=O)C(=O)NC(=N4)N

IUPAC InChI

InChI=1S/C20H21N7O7/c21-19-24-15-14(17(31)25-19)27-11(7-22-15)8-26(20(27)34)10-3-1-9(2-4-10)16(30)23-12(18(32)33)5-6-13(28)29/h1-4,11-12H,5-8H2,(H,23,30)(H,28,29)(H,32,33)(H4,21,22,24,25,31)/t11-,12+/m1/s1

IUPAC InChI key

JSNFRYBHBVDHSG-NEPJUHHUSA-N
LUD

wwPDB Information

Atom count

55 (34 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-03-14

Last modified at

2019-03-22

Status

Released

Obsoleted

Not Assigned



LUD : 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 N1 N N1 N N N 0 7.346 0.426 -0.629
2 C2 C C1 N N N 0 5.083 0.436 0.02
3 N3 N N2 N N N 0 6.403 -1.562 0.241
4 C4 C C2 N N N 0 5.202 -2.382 0.462
5 N5 N N3 N N N 0 -4.361 -0.43 -0.303
6 C6 C C3 N N N 0 2.685 -0.065 0.435
7 C7 C C4 N Y N 0 0.55 -1.221 0.604
8 C9 C C5 N Y N 0 -1.531 -0.218 -0.037
9 N N N4 N N N 0 8.357 2.333 -1.471
10 C C C6 N N N 0 7.253 1.695 -0.966
11 O O O1 N N N 0 2.215 1.004 0.095
12 O6 O O2 N N N 0 3.94 2.391 -0.208
13 C19 C C7 N N N 0 4.99 1.781 -0.336
14 N6 N N5 N N N 0 6.093 2.392 -0.827
15 N2 N N6 N N N 0 3.993 -0.291 0.534
16 N4 N N7 N N N 0 1.934 -1.135 0.747
17 C5 C C8 N N N 0 2.808 -2.202 1.266
18 C3 C C9 R N N 0 4.201 -1.557 1.279
19 C1 C C10 N N N 0 6.295 -0.234 -0.132
20 C12 C C11 N Y N 0 -0.114 -2.387 0.971
21 C11 C C12 N Y N 0 -1.481 -2.474 0.836
22 C10 C C13 N Y N 0 -2.202 -1.388 0.33
23 C8 C C14 N Y N 0 -0.164 -0.139 0.101
24 C13 C C15 N N N 0 -3.668 -1.477 0.185
25 O1 O O3 N N N 0 -4.25 -2.496 0.505
26 C14 C C16 S N N 0 -5.817 -0.518 -0.447
27 C18 C C17 N N N 0 -6.152 -1.168 -1.764
28 O5 O O4 N N N 0 -5.267 -1.522 -2.506
29 O4 O O5 N N N 0 -7.435 -1.355 -2.113
30 C15 C C18 N N N 0 -6.42 0.887 -0.404
31 C16 C C19 N N N 0 -6.187 1.5 0.979
32 C17 C C20 N N N 0 -6.78 2.885 1.021
33 O3 O O6 N N N 0 -6.695 3.617 2.143
34 O2 O O7 N N N 0 -7.333 3.335 0.046
35 H2 H H2 N N N 0 4.759 -2.651 -0.498
36 H3 H H3 N N N 0 5.468 -3.285 1.01
37 H4 H H4 N N N 0 -3.897 0.383 -0.558
38 H5 H H5 N N N 0 -2.086 0.622 -0.428
39 H6 H H6 N N N 0 9.191 1.85 -1.577
40 H7 H H7 N N N 0 8.303 3.268 -1.724
41 H8 H H8 N N N 0 6.056 3.328 -1.079
42 H9 H H9 N N N 0 2.508 -2.486 2.274
43 H10 H H10 N N N 0 2.79 -3.067 0.603
44 H11 H H11 N N N 0 4.565 -1.374 2.29
45 H12 H H12 N N N 0 0.444 -3.226 1.361
46 H13 H H13 N N N 0 -1.996 -3.379 1.12
47 H14 H H14 N N N 0 0.354 0.767 -0.179
48 H15 H H15 N N N 0 -6.227 -1.115 0.368
49 H16 H H16 N N N 0 -7.601 -1.776 -2.968
50 H17 H H17 N N N 0 -5.945 1.51 -1.162
51 H18 H H18 N N N 0 -7.49 0.83 -0.6
52 H19 H H19 N N N 0 -6.661 0.878 1.737
53 H20 H H20 N N N 0 -5.116 1.558 1.175
54 H21 H H21 N N N 0 -7.091 4.499 2.122
55 H1 H H1 N N N 0 7.281 -1.957 0.359



LUD : Chemical Bonds

Total Number of Bonds: 58
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N C N C sing 1.37 N N
2 C N1 C N doub 1.32 N N
3 C N6 C N sing 1.36 N N
4 N1 C1 N C sing 1.34 N N
5 N6 C19 N C sing 1.35 N N
6 C1 C2 C C doub 1.39 N N
7 C1 N3 C N sing 1.38 N N
8 C19 O6 C O doub 1.22 N N
9 C19 C2 C C sing 1.39 N N
10 O C6 O C doub 1.22 N N
11 C2 N2 C N sing 1.41 N N
12 N3 C4 N C sing 1.47 N N
13 C6 N2 C N sing 1.33 N N
14 C6 N4 C N sing 1.34 N N
15 N2 C3 N C sing 1.48 N N
16 C12 C11 C C doub 1.38 N Y
17 C12 C7 C C sing 1.39 N Y
18 C4 C3 C C sing 1.53 N N
19 C11 C10 C C sing 1.4 N Y
20 N4 C7 N C sing 1.39 N N
21 N4 C5 N C sing 1.47 N N
22 C3 C5 C C sing 1.54 N N
23 C7 C8 C C doub 1.39 N Y
24 O1 C13 O C doub 1.22 N N
25 C10 C13 C C sing 1.48 N N
26 C10 C9 C C doub 1.4 N Y
27 C13 N5 C N sing 1.35 N N
28 C8 C9 C C sing 1.38 N Y
29 N5 C14 N C sing 1.47 N N
30 O2 C17 O C doub 1.21 N N
31 C15 C14 C C sing 1.53 N N
32 C15 C16 C C sing 1.53 N N
33 C14 C18 C C sing 1.51 N N
34 C16 C17 C C sing 1.51 N N
35 C17 O3 C O sing 1.34 N N
36 C18 O5 C O doub 1.21 N N
37 C18 O4 C O sing 1.34 N N
38 C4 H2 C H sing 1.09 N N
39 C4 H3 C H sing 1.09 N N
40 N5 H4 N H sing 0.97 N N
41 C9 H5 C H sing 1.08 N N
42 N H6 N H sing 0.97 N N
43 N H7 N H sing 0.97 N N
44 N6 H8 N H sing 0.97 N N
45 C5 H9 C H sing 1.09 N N
46 C5 H10 C H sing 1.09 N N
47 C3 H11 C H sing 1.09 N N
48 C12 H12 C H sing 1.08 N N
49 C11 H13 C H sing 1.08 N N
50 C8 H14 C H sing 1.08 N N
51 C14 H15 C H sing 1.09 N N
52 O4 H16 O H sing 0.97 N N
53 C15 H17 C H sing 1.09 N N
54 C15 H18 C H sing 1.09 N N
55 C16 H19 C H sing 1.09 N N
56 C16 H20 C H sing 1.09 N N
57 O3 H21 O H sing 0.97 N N
58 N3 H1 N H sing 0.97 N N



LUD : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
LUD 6ecq Open in New Window Bound ligand 1 1