Chemical Components in the PDB

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137 : Summary

Code

137

One-letter code

X

Molecule name

1-(O-CARBOXY-PHENYLAMINO)-1-DEOXY-D-RIBULOSE-5-PHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 1-[(2-carboxyphenyl)amino]-1-deoxy-5-O-phosphono-D-arabinitol
OpenEye OEToolkits 1.5.0 2-[[(2R,3S,4R)-2,3,4-trihydroxy-5-phosphonooxy-pentyl]amino]benzoic acid

Formula

C12 H18 N O9 P

Formal charge

0

Molecular weight

351.246 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)OCC(O)C(O)C(O)CNc1ccccc1C(=O)O
SMILES CACTVS 3.341 O[CH](CNc1ccccc1C(O)=O)[CH](O)[CH](O)CO[P](O)(O)=O
SMILES OpenEye OEToolkits 1.5.0 c1ccc(c(c1)C(=O)O)NCC(C(C(COP(=O)(O)O)O)O)O
Canonical SMILES CACTVS 3.341 O[C@H](CNc1ccccc1C(O)=O)[C@H](O)[C@H](O)CO[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1ccc(c(c1)C(=O)O)NC[C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O

IUPAC InChI

InChI=1S/C12H18NO9P/c14-9(11(16)10(15)6-22-23(19,20)21)5-13-8-4-2-1-3-7(8)12(17)18/h1-4,9-11,13-16H,5-6H2,(H,17,18)(H2,19,20,21)/t9-,10-,11+/m1/s1

IUPAC InChI key

AULMJMUNCOBRHC-MXWKQRLJSA-N
137

wwPDB Information

Atom count

41 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2001-06-14

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



137 : Atoms of Molecule

Total Number of Atoms: 41
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 P P P N N N 0 -5.878 0.132 0.032
2 O1P O O1P N N N 0 -5.802 1.265 0.982
3 O2P O O2P N N N 0 -6.056 0.698 -1.465
4 O3P O O3P N N N 0 -7.135 -0.8 0.407
5 O5' O O5' N N N 0 -4.523 -0.734 0.12
6 C5' C C5' N N N 0 -3.44 0.17 -0.106
7 C4' C C4' R N N 0 -2.115 -0.593 -0.035
8 O4' O O4' N N N 0 -2.051 -1.535 -1.107
9 C3' C C3' S N N 0 -0.951 0.394 -0.152
10 O3' O O3' N N N 0 -1.016 1.336 0.92
11 C2' C C2' R N N 0 0.373 -0.369 -0.082
12 O2' O O2' N N N 0 0.408 -1.153 1.113
13 C1' C C1' N N N 0 1.535 0.626 -0.074
14 NH N NH N N N 0 2.804 -0.105 -0.126
15 C1 C C1 N Y N 0 5.223 -0.105 -0.053
16 C2 C C2 N Y N 0 4.005 0.59 -0.129
17 C3 C C3 N Y N 0 4.009 1.978 -0.202
18 C4 C C4 N Y N 0 5.205 2.666 -0.205
19 C5 C C5 N Y N 0 6.409 1.983 -0.135
20 C6 C C6 N Y N 0 6.426 0.608 -0.063
21 C7 C C7 N N N 0 5.233 -1.575 0.025
22 O71 O O71 N N N 0 6.396 -2.233 0.204
23 O72 O O72 N N N 0 4.194 -2.196 -0.074
24 HOP2 H 2HOP N N N 0 -6.101 -0.07 -2.05
25 HOP3 H 3HOP N N N 0 -7.924 -0.244 0.342
26 H5'1 H 1H5' N N N 0 -3.451 0.949 0.657
27 H5'2 H 2H5' N N N 0 -3.545 0.625 -1.091
28 H4' H H4' N N N 0 -2.05 -1.12 0.917
29 HO'4 H 4HO' N N N 0 -2.112 -1.029 -1.928
30 H3' H H3' N N N 0 -1.017 0.921 -1.104
31 HO'3 H 3HO' N N N 0 -0.955 0.83 1.741
32 H2' H H2' N N N 0 0.461 -1.025 -0.948
33 HO'2 H 2HO' N N N 0 0.327 -0.536 1.854
34 H1'1 H 1H1' N N N 0 1.457 1.282 -0.94
35 H1'2 H 2H1' N N N 0 1.497 1.222 0.838
36 HNH H HNH N N N 0 2.804 -1.074 -0.159
37 H3 H H3 N N N 0 3.076 2.518 -0.256
38 H4 H H4 N N N 0 5.203 3.745 -0.261
39 H5 H H5 N N N 0 7.339 2.532 -0.139
40 H6 H H6 N N N 0 7.367 0.081 -0.01
41 HO7 H HO7 N N N 0 6.403 -3.198 0.256



137 : Chemical Bonds

Total Number of Bonds: 41
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P O1P P O doub 1.48 N N
2 P O2P P O sing 1.61 N N
3 P O3P P O sing 1.61 N N
4 P O5' P O sing 1.61 N N
5 O2P HOP2 O H sing 0.97 N N
6 O3P HOP3 O H sing 0.97 N N
7 O5' C5' O C sing 1.43 N N
8 C5' C4' C C sing 1.53 N N
9 C5' H5'1 C H sing 1.09 N N
10 C5' H5'2 C H sing 1.09 N N
11 C4' O4' C O sing 1.43 N N
12 C4' C3' C C sing 1.53 N N
13 C4' H4' C H sing 1.09 N N
14 O4' HO'4 O H sing 0.97 N N
15 C3' O3' C O sing 1.43 N N
16 C3' C2' C C sing 1.53 N N
17 C3' H3' C H sing 1.09 N N
18 O3' HO'3 O H sing 0.97 N N
19 C2' O2' C O sing 1.43 N N
20 C2' C1' C C sing 1.53 N N
21 C2' H2' C H sing 1.09 N N
22 O2' HO'2 O H sing 0.97 N N
23 C1' NH C N sing 1.47 N N
24 C1' H1'1 C H sing 1.09 N N
25 C1' H1'2 C H sing 1.09 N N
26 NH C2 N C sing 1.39 N N
27 NH HNH N H sing 0.97 N N
28 C1 C2 C C doub 1.4 N Y
29 C1 C6 C C sing 1.4 N Y
30 C1 C7 C C sing 1.47 N N
31 C2 C3 C C sing 1.39 N Y
32 C3 C4 C C doub 1.38 N Y
33 C3 H3 C H sing 1.08 N N
34 C4 C5 C C sing 1.39 N Y
35 C4 H4 C H sing 1.08 N N
36 C5 C6 C C doub 1.38 N Y
37 C5 H5 C H sing 1.08 N N
38 C6 H6 C H sing 1.08 N N
39 C7 O71 C O sing 1.35 N N
40 C7 O72 C O doub 1.21 N N
41 O71 HO7 O H sing 0.97 N N



137 : Used in PDB Entries

Total Number of PDB Entries: 7
Ligand Code PDB Entry ID Type Total Distinct
137 1jcm Open in New Window Bound ligand 1 1
137 1lbf Open in New Window Bound ligand 1 1
137 1lbl Open in New Window Bound ligand 1 1
137 1lbm Open in New Window Bound ligand 1 1
137 2y85 Open in New Window Bound ligand 4 1
137 6y88 Open in New Window Bound ligand 7 1
137 7ety Open in New Window Bound ligand 4 1