Chemical Components in the PDB

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1DP : Summary

Code

1DP

One-letter code

X

Molecule name

N1-deaza-adenosine-5'-monophosphate

Synonyms

3-(5-O-phosphono-beta-D-ribofuranosyl)-3H-imidazo[4,5-b]pyridin-7-amine

Systematic names

ProgramVersionName
ACDLabs 10.04 3-(5-O-phosphono-beta-D-ribofuranosyl)-3H-imidazo[4,5-b]pyridin-7-amine
OpenEye OEToolkits 1.5.0 [(2R,3S,4R,5R)-5-(7-aminoimidazo[5,4-b]pyridin-3-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C11 H15 N4 O7 P

Formal charge

0

Molecular weight

346.233 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)OCC3OC(n2cnc1c(N)ccnc12)C(O)C3O
SMILES CACTVS 3.341 Nc1ccnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
SMILES OpenEye OEToolkits 1.5.0 c1cnc2c(c1N)ncn2C3C(C(C(O3)COP(=O)(O)O)O)O
Canonical SMILES CACTVS 3.341 Nc1ccnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1cnc2c(c1N)ncn2[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O

IUPAC InChI

InChI=1S/C11H15N4O7P/c12-5-1-2-13-10-7(5)14-4-15(10)11-9(17)8(16)6(22-11)3-21-23(18,19)20/h1-2,4,6,8-9,11,16-17H,3H2,(H2,12,13)(H2,18,19,20)/t6-,8-,9-,11-/m1/s1

IUPAC InChI key

MKNCBTMEOTYSIQ-PNHWDRBUSA-N
1DP

wwPDB Information

Atom count

38 (23 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA LINKING

Type code

ATOMN

Is modified

No

Standard parent

Not Assigned

Defined at

2009-07-01

Last modified at

2021-03-13

Status

Released

Obsoleted

Not Assigned



1DP : Atoms of Molecule

Total Number of Atoms: 38
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O3P O O3P N N Y 0 -5.13 2.082 -1.237
2 P P P N N N 0 -4.753 1.026 -0.081
3 O1P O O1P N N N 0 -4.53 1.746 1.192
4 O2P O O2P N N N 0 -5.96 -0.024 0.101
5 O5' O O5' N N N 0 -3.412 0.236 -0.493
6 C5' C C5' N N N 0 -2.761 -0.697 0.372
7 C4' C C4' R N N 0 -1.523 -1.262 -0.327
8 O4' O O4' N N N 0 -0.548 -0.222 -0.511
9 C1' C C1' R N N 0 0.753 -0.835 -0.38
10 N9 N N9 N Y N 0 1.766 0.17 -0.051
11 C4 C C4 N Y N 0 3.119 0.073 -0.292
12 N3 N N3 N Y N 0 3.888 -0.856 -0.842
13 C2 C C2 N Y N 0 5.192 -0.7 -0.956
14 C1 C C1 N Y N 0 5.823 0.445 -0.507
15 C6 C C6 N Y N 0 5.069 1.456 0.079
16 N6 N N6 N N N 0 5.671 2.621 0.543
17 C5 C C5 N Y N 0 3.681 1.266 0.19
18 N7 N N7 N Y N 0 2.667 2.014 0.69
19 C8 C C8 N Y N 0 1.543 1.375 0.545
20 C2' C C2' R N N 0 0.566 -1.831 0.793
21 O2' O O2' N N N 0 1.511 -2.9 0.71
22 C3' C C3' S N N 0 -0.874 -2.347 0.554
23 O3' O O3' N N Y 0 -0.849 -3.6 -0.133
24 HO3P H HO3P N N Y 0 -5.93 2.595 -1.055
25 HO2P H HO2P N N N 0 -6.162 -0.533 -0.696
26 H5' H H5' N N N 0 -2.461 -0.192 1.29
27 H5'A H H5'A N N N 0 -3.446 -1.51 0.611
28 H4' H H4' N N N 0 -1.802 -1.683 -1.293
29 H1' H H1' N N N 0 1.022 -1.364 -1.294
30 H2 H H2 N N N 0 5.78 -1.484 -1.41
31 H1 H H1 N N N 0 6.893 0.553 -0.609
32 HN6 H HN6 N N N 0 6.63 2.738 0.46
33 HN6A H HN6A N N N 0 5.131 3.317 0.95
34 H8 H H8 N N N 0 0.576 1.744 0.853
35 H2' H H2' N N N 0 0.642 -1.32 1.753
36 HO2' H HO2' N N N 0 1.434 -3.549 1.422
37 H3' H H3' N N N 0 -1.407 -2.44 1.5
38 HO3' H HO3' N N Y 0 -0.399 -4.306 0.352



1DP : 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 P O3P P O sing 1.61 N N
2 O3P HO3P O H sing 0.97 N N
3 O5' P O P sing 1.61 N N
4 O1P P O P doub 1.48 N N
5 P O2P P O sing 1.61 N N
6 O2P HO2P O H sing 0.97 N N
7 O5' C5' O C sing 1.43 N N
8 C4' C5' C C sing 1.53 N N
9 C5' H5' C H sing 1.09 N N
10 C5' H5'A C H sing 1.09 N N
11 C3' C4' C C sing 1.54 N N
12 C4' O4' C O sing 1.44 N N
13 C4' H4' C H sing 1.09 N N
14 C1' O4' C O sing 1.44 N N
15 C2' C1' C C sing 1.55 N N
16 N9 C1' N C sing 1.46 N N
17 C1' H1' C H sing 1.09 N N
18 C4 N9 C N sing 1.38 N Y
19 N9 C8 N C sing 1.36 N Y
20 N3 C4 N C doub 1.33 N Y
21 C4 C5 C C sing 1.4 N Y
22 C2 N3 C N sing 1.32 N Y
23 C1 C2 C C doub 1.38 N Y
24 C2 H2 C H sing 1.08 N N
25 C1 C6 C C sing 1.39 N Y
26 C1 H1 C H sing 1.08 N N
27 N6 C6 N C sing 1.39 N N
28 C6 C5 C C doub 1.41 N Y
29 N6 HN6 N H sing 0.97 N N
30 N6 HN6A N H sing 0.97 N N
31 C5 N7 C N sing 1.36 N Y
32 N7 C8 N C doub 1.3 N Y
33 C8 H8 C H sing 1.08 N N
34 O2' C2' O C sing 1.43 N N
35 C2' C3' C C sing 1.55 N N
36 C2' H2' C H sing 1.09 N N
37 O2' HO2' O H sing 0.97 N N
38 O3' C3' O C sing 1.43 N N
39 C3' H3' C H sing 1.09 N N
40 O3' HO3' O H sing 0.97 N N



1DP : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
1DP 3i2q Open in New Window Polymer component 1 1
1DP 3i2r Open in New Window Polymer component 1 1
1DP 3i2s Open in New Window Polymer component 1 1
1DP 3i2u Open in New Window Polymer component 1 1