Chemical Components in the PDB

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3DR : Summary

Code

3DR

One-letter code

N

Molecule name

1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE

Synonyms

ABASIC DIDEOXYRIBOSE

Systematic names

ProgramVersionName
ACDLabs 10.04 1,4-anhydro-2-deoxy-5-O-phosphono-D-erythro-pentitol
OpenEye OEToolkits 1.5.0 [(2R,3S)-3-hydroxyoxolan-2-yl]methyl dihydrogen phosphate

Formula

C5 H11 O6 P

Formal charge

0

Molecular weight

198.111 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(OCC1OCCC1O)(O)O
SMILES CACTVS 3.341 O[CH]1CCO[CH]1CO[P](O)(O)=O
SMILES OpenEye OEToolkits 1.5.0 C1COC(C1O)COP(=O)(O)O
Canonical SMILES CACTVS 3.341 O[C@H]1CCO[C@@H]1CO[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C1CO[C@@H]([C@H]1O)COP(=O)(O)O

IUPAC InChI

InChI=1S/C5H11O6P/c6-4-1-2-10-5(4)3-11-12(7,8)9/h4-6H,1-3H2,(H2,7,8,9)/t4-,5+/m0/s1

IUPAC InChI key

BVOBPNSQIRMLCA-CRCLSJGQSA-N
3DR

wwPDB Information

Atom count

23 (12 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



3DR : Atoms of Molecule

Total Number of Atoms: 23
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O5' O O5* N N N 0 -0.442 0.55 -0.918
2 P P P N N N 0 -0.015 -0.051 -2.349
3 OP1 O O1P N N N 0 -0.29 -1.505 -2.375
4 OP2 O O2P N N N 0 -0.861 0.675 -3.51
5 OP3 O O3P N N Y 0 1.556 0.202 -2.59
6 C2' C C2* N N N 0 -0.26 -0.503 3.709
7 C5' C C5* N N N 0 0.338 -0.131 0.065
8 C4' C C4* R N N 0 -0.02 0.396 1.456
9 O4' O O4* N N N 0 -1.415 0.144 1.745
10 C1' C C1* N N N 0 -1.525 0.209 3.184
11 C3' C C3* S N N 0 0.751 -0.377 2.548
12 O3' O O3* N N N 0 1.902 0.36 2.965
13 HOP2 H 2HOP N N N 0 -0.575 0.287 -4.349
14 HOP3 H 3HOP N N N 0 1.691 1.159 -2.566
15 H2' H 1H2* N N N 0 -0.471 -1.552 3.918
16 H2'' H 2H2* N N N 0 0.117 -0.004 4.601
17 H1'1 H 1H1* N N N 0 -2.422 -0.312 3.519
18 H5' H 1H5* N N N 0 1.397 0.042 -0.126
19 H5'' H 2H5* N N N 0 0.13 -1.2 0.017
20 H4'1 H 1H4* N N N 0 0.194 1.462 1.524
21 H1'2 H 2H1* N N N 0 -1.542 1.246 3.517
22 H3' H H3* N N N 0 1.041 -1.363 2.185
23 HO3' H HO3* N N Y 0 2.325 -0.154 3.665



3DR : Chemical Bonds

Total Number of Bonds: 23
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O5' P O P sing 1.61 N N
2 O5' C5' O C sing 1.43 N N
3 P OP1 P O doub 1.48 N N
4 P OP2 P O sing 1.61 N N
5 P OP3 P O sing 1.61 N N
6 OP2 HOP2 O H sing 0.97 N N
7 OP3 HOP3 O H sing 0.97 N N
8 C2' C1' C C sing 1.54 N N
9 C2' C3' C C sing 1.54 N N
10 C2' H2' C H sing 1.09 N N
11 C2' H2'' C H sing 1.09 N N
12 C5' C4' C C sing 1.53 N N
13 C5' H5' C H sing 1.09 N N
14 C5' H5'' C H sing 1.09 N N
15 C4' O4' C O sing 1.45 N N
16 C4' C3' C C sing 1.54 N N
17 C4' H4'1 C H sing 1.09 N N
18 O4' C1' O C sing 1.44 N N
19 C1' H1'1 C H sing 1.09 N N
20 C1' H1'2 C H sing 1.09 N N
21 C3' O3' C O sing 1.43 N N
22 C3' H3' C H sing 1.09 N N
23 O3' HO3' O H sing 0.97 N N



3DR : Used in PDB Entries

Total Number of PDB Entries: 176
Ligand Code PDB Entry ID Type Total Distinct
3DR 1de8 Open in New Window Polymer component 2 1
3DR 1de9 Open in New Window Polymer component 2 1
3DR 1dew Open in New Window Polymer component 2 1
3DR 1fn7 Open in New Window Polymer component 1 1
3DR 1fzl Open in New Window Polymer component 1 1
3DR 1fzs Open in New Window Polymer component 1 1
3DR 1ht4 Open in New Window Polymer component 2 2
3DR 1ht7 Open in New Window Polymer component 2 2
3DR 1ixy Open in New Window Polymer component 2 1
3DR 1m06 Open in New Window Polymer component 10 10
3DR 1m5r Open in New Window Polymer component 2 1
3DR 1n39 Open in New Window Polymer component 1 1
3DR 1n3a Open in New Window Polymer component 1 1
3DR 1n48 Open in New Window Polymer component 1 1
3DR 1n56 Open in New Window Polymer component 2 1
3DR 1oe4 Open in New Window Polymer component 1 1
3DR 1oe5 Open in New Window Polymer component 2 2
3DR 1oe6 Open in New Window Polymer component 1 1
3DR 1p59 Open in New Window Polymer component 1 1
3DR 1p5w Open in New Window Polymer component 1 1
3DR 1ph5 Open in New Window Polymer component 1 1
3DR 1phj Open in New Window Polymer component 1 1
3DR 1pjj Open in New Window Polymer component 1 1
3DR 1pm5 Open in New Window Polymer component 1 1
3DR 1q9x Open in New Window Bound ligand 4 1
3DR 1qum Open in New Window Polymer component 1 1
3DR 1y6f Open in New Window Polymer component 1 1
3DR 1yct Open in New Window Polymer component 2 2
3DR 1ycw Open in New Window Polymer component 2 2
3DR 2dtu Open in New Window Polymer component 4 1
3DR 2ibt Open in New Window Polymer component 2 1
3DR 2ih5 Open in New Window Polymer component 1 1
3DR 2kh0 Open in New Window Polymer component 2 2
3DR 2kh1 Open in New Window Polymer component 2 2
3DR 2l2u Open in New Window Polymer component 2 2
3DR 2l2v Open in New Window Polymer component 2 2
3DR 2m40 Open in New Window Polymer component 1 1
3DR 2np6 Open in New Window Polymer component 2 1
3DR 2np7 Open in New Window Polymer component 1 1
3DR 2nq9 Open in New Window Polymer component 1 1
3DR 2nqj Open in New Window Polymer component 1 1
3DR 2ofi Open in New Window Polymer component 1 1
3DR 2oyq Open in New Window Polymer component 4 1
3DR 2ozm Open in New Window Polymer component 1 1
3DR 2p5g Open in New Window Polymer component 4 1
3DR 2p5o Open in New Window Polymer component 4 1
3DR 2p66 Open in New Window Polymer component 1 1
3DR 2rba Open in New Window Polymer component 1 1
3DR 3a46 Open in New Window Polymer component 2 1
3DR 3ei2 Open in New Window Polymer component 1 1
3DR 3g6v Open in New Window Polymer component 1 1
3DR 3g6x Open in New Window Polymer component 1 1
3DR 3g6y Open in New Window Polymer component 1 1
3DR 3isc Open in New Window Polymer component 1 1
3DR 3isd Open in New Window Polymer component 1 1
3DR 3jxz Open in New Window Polymer component 1 1
3DR 3jy1 Open in New Window Polymer component 1 1
3DR 3k5l Open in New Window Polymer component 1 1
3DR 3k5m Open in New Window Polymer component 1 1
3DR 3k5n Open in New Window Polymer component 1 1
3DR 3lwl Open in New Window Polymer component 1 1
3DR 3osp Open in New Window Polymer component 1 1
3DR 3po5 Open in New Window Polymer component 1 1
3DR 3rr7 Open in New Window Polymer component 1 1
3DR 3rr8 Open in New Window Polymer component 1 1
3DR 3rrg Open in New Window Polymer component 1 1
3DR 3rrh Open in New Window Polymer component 1 1
3DR 3s6i Open in New Window Polymer component 2 1
3DR 3t3f Open in New Window Polymer component 1 1
3DR 3twm Open in New Window Polymer component 2 1
3DR 4a0k Open in New Window Polymer component 1 1
3DR 4a0l Open in New Window Polymer component 2 1
3DR 4b21 Open in New Window Polymer component 1 1
3DR 4b22 Open in New Window Polymer component 1 1
3DR 4b23 Open in New Window Polymer component 1 1
3DR 4b24 Open in New Window Polymer component 1 1
3DR 4b3o Open in New Window Polymer component 1 1
3DR 4b5f Open in New Window Polymer component 1 1
3DR 4b5g Open in New Window Polymer component 3 1
3DR 4b5h Open in New Window Polymer component 1 1
3DR 4b5i Open in New Window Polymer component 1 1
3DR 4b5j Open in New Window Polymer component 1 1
3DR 4b5m Open in New Window Polymer component 3 1
3DR 4dk9 Open in New Window Polymer component 1 1
3DR 4dtj Open in New Window Polymer component 1 1
3DR 4dtm Open in New Window Polymer component 1 1
3DR 4dtn Open in New Window Polymer component 1 1
3DR 4dto Open in New Window Polymer component 1 1
3DR 4dtp Open in New Window Polymer component 1 1
3DR 4dtr Open in New Window Polymer component 1 1
3DR 4dts Open in New Window Polymer component 1 1
3DR 4dtu Open in New Window Polymer component 1 1
3DR 4dtx Open in New Window Polymer component 1 1
3DR 4e54 Open in New Window Polymer component 1 1
3DR 4e5z Open in New Window Polymer component 1 1
3DR 4e9f Open in New Window Polymer component 1 1
3DR 4ejy Open in New Window Polymer component 2 1
3DR 4ejz Open in New Window Polymer component 2 1
3DR 4ew4 Open in New Window Polymer component 1 1
3DR 4hsb Open in New Window Polymer component 1 1
3DR 4iem Open in New Window Polymer component 4 1
3DR 4lz1 Open in New Window Polymer component 1 1
3DR 4lz4 Open in New Window Polymer component 2 1
3DR 4nrw Open in New Window Polymer component 2 1
3DR 4pcz Open in New Window Polymer component 1 1
3DR 4pd2 Open in New Window Polymer component 1 1
3DR 4pdg Open in New Window Polymer component 1 1
3DR 4rnm Open in New Window Polymer component 1 1
3DR 4rnn Open in New Window Polymer component 1 1
3DR 4rno Open in New Window Polymer component 1 1
3DR 5ciy Open in New Window Polymer component 1 1
3DR 5cle Open in New Window Polymer component 1 1
3DR 5dff Open in New Window Polymer component 1 1
3DR 5dfh Open in New Window Polymer component 1 1
3DR 5dfj Open in New Window Polymer component 1 1
3DR 5ew1 Open in New Window Polymer component 1 1
3DR 5ew2 Open in New Window Polymer component 1 1
3DR 5ink Open in New Window Polymer component 2 1
3DR 5jrg Open in New Window Polymer component 2 2
3DR 5vi0 Open in New Window Polymer component 2 1
3DR 6blo Open in New Window Polymer component 1 1
3DR 6blp Open in New Window Polymer component 1 1
3DR 6bm2 Open in New Window Polymer component 1 1
3DR 6bm4 Open in New Window Polymer component 1 1
3DR 6bor Open in New Window Polymer component 1 1
3DR 6bov Open in New Window Polymer component 1 1
3DR 6bqf Open in New Window Polymer component 1 1
3DR 6bsg Open in New Window Polymer component 1 1
3DR 6bsh Open in New Window Polymer component 1 1
3DR 6bsi Open in New Window Polymer component 1 1
3DR 6bsj Open in New Window Polymer component 1 1
3DR 6kbz Open in New Window Polymer component 4 1
3DR 6ki3 Open in New Window Polymer component 2 1
3DR 6lrd Open in New Window Polymer component 1 1
3DR 6m6j Open in New Window Polymer component 1 1
3DR 6m6k Open in New Window Polymer component 1 1
3DR 6p93 Open in New Window Polymer component 1 1
3DR 6p94 Open in New Window Polymer component 1 1
3DR 6r8z Open in New Window Polymer component 2 2
3DR 6r90 Open in New Window Polymer component 2 2
3DR 6r91 Open in New Window Polymer component 2 2
3DR 6r92 Open in New Window Polymer component 2 2
3DR 6r94 Open in New Window Polymer component 2 3
3DR 6rnm Open in New Window Polymer component 1 1
3DR 6rno Open in New Window Polymer component 1 1
3DR 6rnr Open in New Window Polymer component 1 1
3DR 6ro2 Open in New Window Polymer component 1 1
3DR 6rok Open in New Window Polymer component 1 1
3DR 6rp0 Open in New Window Polymer component 2 1
3DR 6rp7 Open in New Window Polymer component 1 1
3DR 6tc9 Open in New Window Polymer component 2 1
3DR 6ueu Open in New Window Polymer component 2 1
3DR 6w0q Open in New Window Polymer component 1 1
3DR 6w2p Open in New Window Polymer component 1 1
3DR 6w43 Open in New Window Polymer component 1 1
3DR 6w4i Open in New Window Polymer component 2 1
3DR 7bsh Open in New Window Polymer component 2 1
3DR 7d0x Open in New Window Polymer component 1 1
3DR 7ef8 Open in New Window Polymer component 1 1
3DR 7ef9 Open in New Window Polymer component 1 1
3DR 7k32 Open in New Window Polymer component 1 1
3DR 7k33 Open in New Window Polymer component 1 1
3DR 7r6t Open in New Window Polymer component 3 1
3DR 7tr7 Open in New Window Polymer component 2 1
3DR 7u50 Open in New Window Polymer component 1 1
3DR 7u51 Open in New Window Polymer component 1 1
3DR 7u52 Open in New Window Polymer component 1 1
3DR 7u53 Open in New Window Polymer component 1 1
3DR 8ebv Open in New Window Polymer component 2 2
3DR 8ebw Open in New Window Polymer component 2 2
3DR 8ebx Open in New Window Polymer component 2 2
3DR 8ka3 Open in New Window Bound ligand 1 1
3DR 8ka5 Open in New Window Bound ligand 1 1
3DR 8qhr Open in New Window Bound ligand 2 1
3DR 8th9 Open in New Window Polymer component 1 1
3DR 9mht Open in New Window Polymer component 1 1