Chemical Components in the PDB

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1XL : Summary

Code

1XL

One-letter code

X

Molecule name

1-deoxy-1-[6-(hydroxymethyl)-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl]-D-arabinitol

Systematic names

ProgramVersionName
ACDLabs 12.01 1-deoxy-1-[6-(hydroxymethyl)-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl]-D-arabinitol
OpenEye OEToolkits 1.7.6 6-(hydroxymethyl)-8-[(2R,3S,4R)-2,3,4,5-tetrakis(oxidanyl)pentyl]pteridine-2,4-dione

Formula

C12 H16 N4 O7

Formal charge

0

Molecular weight

328.278 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C1C2=NC(=CN(C2=NC(=O)N1)CC(O)C(O)C(O)CO)CO
SMILES CACTVS 3.385 OC[CH](O)[CH](O)[CH](O)CN1C=C(CO)N=C2C(=O)NC(=O)N=C12
SMILES OpenEye OEToolkits 1.7.6 C1=C(N=C2C(=O)NC(=O)N=C2N1CC(C(C(CO)O)O)O)CO
Canonical SMILES CACTVS 3.385 OC[C@@H](O)[C@@H](O)[C@H](O)CN1C=C(CO)N=C2C(=O)NC(=O)N=C12
Canonical SMILES OpenEye OEToolkits 1.7.6 C1=C(N=C2C(=O)NC(=O)N=C2N1C[C@H]([C@@H]([C@@H](CO)O)O)O)CO

IUPAC InChI

InChI=1S/C12H16N4O7/c17-3-5-1-16(2-6(19)9(21)7(20)4-18)10-8(13-5)11(22)15-12(23)14-10/h1,6-7,9,17-21H,2-4H2,(H,15,22,23)/t6-,7-,9+/m1/s1

IUPAC InChI key

RTNMDIMJQSRAGT-BHNWBGBOSA-N
1XL

wwPDB Information

Atom count

39 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-07-29

Last modified at

2013-10-11

Status

Released

Obsoleted

Not Assigned



1XL : Atoms of Molecule

Total Number of Atoms: 39
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OAD O OAD N N N 0 -6.523 -0.075 -0.899
2 CAJ C CAJ N N N 0 -5.577 0.199 0.137
3 CAT C CAT R N N 0 -4.168 0.24 -0.457
4 OAE O OAE N N N 0 -4.065 1.339 -1.364
5 CAV C CAV S N N 0 -3.145 0.41 0.668
6 OAG O OAG N N N 0 -3.248 -0.69 1.575
7 CAU C CAU R N N 0 -1.735 0.45 0.074
8 OAF O OAF N N N 0 -1.52 -0.717 -0.721
9 CAK C CAK N N N 0 -0.706 0.494 1.205
10 N8 N N8 N N N 0 0.635 0.654 0.639
11 C7 C C7 N N N 0 1.151 1.882 0.431
12 C8A C C8A N N N 0 1.387 -0.438 0.318
13 N1 N N1 N N N 0 0.941 -1.673 0.501
14 C2 C C2 N N N 0 1.675 -2.735 0.186
15 O2 O O2 N N N 0 1.205 -3.843 0.38
16 N3 N N3 N N N 0 2.909 -2.648 -0.335
17 C4 C C4 N N N 0 3.475 -1.441 -0.569
18 O4 O O4 N N N 0 4.593 -1.347 -1.041
19 C4A C C4A N N N 0 2.684 -0.243 -0.229
20 N5 N N5 N N N 0 3.148 0.977 -0.422
21 C6 C C6 N N N 0 2.413 2.029 -0.101
22 CAI C CAI N N N 0 2.967 3.413 -0.324
23 OAC O OAC N N N 0 4.098 3.616 0.525
24 H1 H H1 N N N 0 -7.439 -0.116 -0.594
25 H2 H H2 N N N 0 -5.807 1.162 0.593
26 H3 H H3 N N N 0 -5.63 -0.583 0.893
27 H4 H H4 N N N 0 -3.971 -0.69 -0.99
28 H5 H H5 N N N 0 -4.228 2.201 -0.958
29 H6 H H6 N N N 0 -3.342 1.34 1.201
30 H7 H H7 N N N 0 -3.085 -1.552 1.168
31 H8 H H8 N N N 0 -1.629 1.339 -0.549
32 H9 H H9 N N N 0 -1.599 -1.547 -0.231
33 H10 H H10 N N N 0 -0.925 1.336 1.863
34 H11 H H11 N N N 0 -0.753 -0.434 1.775
35 H12 H H12 N N N 0 0.571 2.757 0.684
36 H14 H H14 N N N 0 3.4 -3.458 -0.546
37 H15 H H15 N N N 0 3.27 3.52 -1.366
38 H16 H H16 N N N 0 2.2 4.152 -0.091
39 H17 H H17 N N N 0 4.506 4.488 0.434



1XL : 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 O2 C2 O C doub 1.219098 N N
2 C2 N3 C N sing 1.3422987 N N
3 C2 N1 C N sing 1.3288435 N N
4 N3 C4 N C sing 1.3534995 N N
5 N1 C8A N C doub 1.3257564 N N
6 C4 O4 C O doub 1.2171869 N N
7 C4 C4A C C sing 1.4752915 N N
8 C8A C4A C C sing 1.421071 N N
9 C8A N8 C N sing 1.3641881 N N
10 CAK N8 C N sing 1.4643214 N N
11 CAK CAU C C sing 1.5296856 N N
12 C4A N5 C N doub 1.3194487 N N
13 N8 C7 N C sing 1.3481483 N N
14 N5 C6 N C sing 1.3228643 N N
15 OAF CAU O C sing 1.4283344 N N
16 OAG CAV O C sing 1.4294257 N N
17 C7 C6 C C doub 1.3774167 N N
18 C6 CAI C C sing 1.507349 N N
19 CAU CAV C C sing 1.5305345 N N
20 OAC CAI O C sing 1.4286956 N N
21 CAV CAT C C sing 1.5300503 N N
22 OAE CAT O C sing 1.4286563 N N
23 CAT CAJ C C sing 1.5296398 N N
24 CAJ OAD C O sing 1.4294362 N N
25 OAD H1 O H sing 0.9663136 N N
26 CAJ H2 C H sing 1.0900482 N N
27 CAJ H3 C H sing 1.0889761 N N
28 CAT H4 C H sing 1.0898615 N N
29 OAE H5 O H sing 0.966669 N N
30 CAV H6 C H sing 1.0898615 N N
31 OAG H7 O H sing 0.9670895 N N
32 CAU H8 C H sing 1.0907273 N N
33 OAF H9 O H sing 0.96707857 N N
34 CAK H10 C H sing 1.0908203 N N
35 CAK H11 C H sing 1.0900885 N N
36 C7 H12 C H sing 1.0798305 N N
37 N3 H14 N H sing 0.9704133 N N
38 CAI H15 C H sing 1.0904229 N N
39 CAI H16 C H sing 1.0902747 N N
40 OAC H17 O H sing 0.9670207 N N



1XL : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
1XL 4lcc Open in New Window Bound ligand 1 1