Chemical Components in the PDB

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SCA : Summary

Code

SCA

One-letter code

X

Molecule name

SUCCINYL-COENZYME A

Systematic names

ProgramVersionName
ACDLabs 10.04 (3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-10,14,19-trioxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphadocosan-22-oic acid 3,5-dioxide (non-preferred name)
OpenEye OEToolkits 1.5.0 4-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-2-hydroxy-3,3-dimethyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-4-oxo-butanoic acid

Formula

C25 H40 N7 O19 P3 S

Formal charge

0

Molecular weight

867.607 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)CCC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
SMILES CACTVS 3.341 CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCSC(=O)CCC(O)=O
SMILES OpenEye OEToolkits 1.5.0 CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC(=O)CCC(=O)O)O
Canonical SMILES CACTVS 3.341 CC(C)(CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)CCC(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CC(C)(CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSC(=O)CCC(=O)O)O

IUPAC InChI

InChI=1S/C25H40N7O19P3S/c1-25(2,20(38)23(39)28-6-5-14(33)27-7-8-55-16(36)4-3-15(34)35)10-48-54(45,46)51-53(43,44)47-9-13-19(50-52(40,41)42)18(37)24(49-13)32-12-31-17-21(26)29-11-30-22(17)32/h11-13,18-20,24,37-38H,3-10H2,1-2H3,(H,27,33)(H,28,39)(H,34,35)(H,43,44)(H,45,46)(H2,26,29,30)(H2,40,41,42)/t13-,18-,19-,20+,24-/m1/s1

IUPAC InChI key

VNOYUJKHFWYWIR-ITIYDSSPSA-N
SCA

wwPDB Information

Atom count

95 (55 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



SCA : Atoms of Molecule

Total Number of Atoms: 95
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1' C C1' R N N 0 -2.313 -0.605 -6.563
2 C2 C C2 N Y N 0 -6.33 -1.963 -8.035
3 C2' C C2' R N N 0 -2.176 0.896 -6.922
4 C3' C C3' S N N 0 -0.637 1.076 -6.988
5 C4 C C4 N Y N 0 -4.752 -1.279 -6.51
6 C4' C C4' R N N 0 -0.087 -0.104 -6.165
7 C5 C C5 N Y N 0 -5.706 -1.399 -5.485
8 C5' C C5' N N N 0 0.761 0.419 -5.004
9 C6 C C6 N Y N 0 -7.002 -1.817 -5.831
10 C8 C C8 N Y N 0 -3.855 -0.737 -4.57
11 CP1 C CP1 N N N 0 -0.977 0.338 9.251
12 CP2 C CP2 N N N 0 0.067 1.069 8.405
13 CP3 C CP3 N N N 0 1.861 0.506 6.855
14 CP4 C CP4 N N N 0 2.689 -0.5 6.099
15 CP5 C CP5 N N N 0 3.734 0.229 5.253
16 CP6 C CP6 N N N 0 5.527 -0.333 3.703
17 CP7 C CP7 R N N 0 6.408 -1.341 3.011
18 CP8 C CP8 N N N 0 6.535 -2.977 1.127
19 CP9 C CP9 N N N 0 4.502 -2.896 2.577
20 CPA C CPA N N N 0 5.606 -2.061 1.926
21 CPB C CPB N N N 0 4.977 -1.029 0.987
22 CS1 C CS1 N N N 0 -3.028 0.495 10.997
23 CS2 C CS2 N N N 0 -4.079 1.058 11.918
24 CS3 C CS3 N N N 0 -4.883 -0.086 12.537
25 CS4 C CS4 N N N 0 -5.934 0.476 13.458
26 H1' H H1' N N N 0 -2.209 -1.223 -7.454
27 H11 H 1H1 N N N 0 -1.625 -0.248 8.6
28 H12 H 2H1 N N N 0 -0.475 -0.322 9.957
29 H2 H H2 N N N 0 -6.584 -2.19 -9.059
30 H2' H H2' N N N 0 -2.609 1.523 -6.143
31 H21 H 1H2 N N N 0 0.715 1.656 9.056
32 H22 H 2H2 N N N 0 -0.434 1.73 7.699
33 H3' H H3' N N N 0 -0.344 2.024 -6.537
34 H4' H H4' N N N 0 0.515 -0.751 -6.802
35 H41 H 1H4 N N N 0 2.041 -1.088 5.448
36 H42 H 2H4 N N N 0 3.19 -1.162 6.805
37 H5'1 H 1H5' N N N 0 0.148 1.055 -4.365
38 H5'2 H 2H5' N N N 0 1.597 0.998 -5.398
39 H51 H 1H5 N N N 0 4.381 0.817 5.904
40 H52 H 2H5 N N N 0 3.232 0.89 4.547
41 H7 H H7 N N N 0 6.769 -2.068 3.739
42 H8 H H8 N N N 0 -3.139 -0.422 -3.826
43 H81 H 1H8 N N N 0 7.359 -2.392 0.719
44 H82 H 2H8 N N N 0 6.93 -3.754 1.782
45 H83 H 3H8 N N N 0 5.977 -3.438 0.312
46 H91 H 1H9 N N N 0 3.771 -2.234 3.042
47 H92 H 2H9 N N N 0 4.01 -3.504 1.818
48 H93 H 3H9 N N N 0 4.938 -3.546 3.336
49 HN1 H HN1 N N N 0 0.693 -0.858 7.77
50 HN2 H HN2 N N N 0 4.359 -1.697 4.618
51 HN61 H 1HN6 N N N 0 -8.876 -2.237 -5.117
52 HN62 H 2HN6 N N N 0 -7.783 -1.748 -3.938
53 HO2' H 'HO2 N N N 0 -3.714 0.955 -8.109
54 HO3 H HO3 N N N 0 7.16 -0.039 1.78
55 HO4 H HO4 N N N 0 -7.437 0.012 14.707
56 HOB H HOB N N N 0 0.499 0.334 -1.787
57 HOM H HOM N N N 0 5.33 -0.298 -2.137
58 HOW H HOW N N N 0 1.545 3.235 -10.316
59 HOX H HOX N N N 0 -1.193 3.469 -9.082
60 HPB1 H 1HPB N N N 0 4.315 -0.376 1.556
61 HPB2 H 2HPB N N N 0 5.764 -0.434 0.523
62 HS21 H 1HS2 N N N 0 -3.598 1.633 12.71
63 HS22 H 2HS2 N N N 0 -4.748 1.707 11.353
64 HS31 H 1HS3 N N N 0 -5.364 -0.661 11.746
65 HS32 H 2HS3 N N N 0 -4.214 -0.735 13.102
66 N1 N N1 N Y N 0 -7.262 -2.084 -7.107
67 N3 N N3 N Y N 0 -5.103 -1.574 -7.757
68 N6 N N6 N N N 0 -7.985 -1.947 -4.866
69 N7 N N7 N Y N 0 -5.095 -1.05 -4.328
70 N9 N N9 N Y N 0 -3.593 -0.866 -5.902
71 NP1 N NP1 N N N 0 0.872 0.089 7.67
72 NP2 N NP2 N N N 0 4.538 -0.749 4.518
73 O11 O O11 N N N 0 1.21 0.89 -2.136
74 O12 O O12 N N N 0 3.251 0.734 -3.612
75 O2' O O2' N N N 0 -2.775 1.174 -8.189
76 O21 O O21 N N N 0 2.722 0.319 -0.167
77 O22 O O22 N N N 0 4.784 0.311 -1.623
78 O3' O O3' N N N 0 -0.182 1.006 -8.341
79 O31 O O31 N N N 0 1.704 2.564 -7.724
80 O32 O O32 N N N 0 1.105 2.387 -10.17
81 O33 O O33 N N N 0 -0.468 3.616 -8.46
82 O4' O O4' N N N 0 -1.215 -0.835 -5.654
83 O5' O O5' N N N 0 1.26 -0.681 -4.243
84 O6 O O6 N N N 0 2.735 -1.251 -2.143
85 O7 O O7 N N N 0 4.227 -1.701 -0.026
86 OP1 O OP1 N N N 0 2.085 1.691 6.729
87 OP2 O OP2 N N N 0 5.708 0.852 3.525
88 OP3 O OP3 N N N 0 7.521 -0.672 2.415
89 OS1 O OS1 N N N 0 -2.931 -0.705 10.85
90 OS4 O OS4 N N N 0 -6.763 -0.349 14.116
91 OS5 O OS5 N N N 0 -6.03 1.672 13.605
92 P1 P P1 R N N 0 2.138 -0.059 -3.046
93 P2 P P2 R N N 0 3.598 -0.561 -0.972
94 P3 P P3 N N N 0 0.565 2.397 -8.653
95 S S S N N N 0 -1.971 1.548 10.159



SCA : Chemical Bonds

Total Number of Bonds: 97
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C8 N9 C N sing 1.36 N Y
2 C8 N7 C N doub 1.3 N Y
3 C8 H8 C H sing 1.08 N N
4 N9 C4 N C sing 1.37 N Y
5 N9 C1' N C sing 1.46 N N
6 C4 C5 C C sing 1.41 N Y
7 C4 N3 C N doub 1.33 N Y
8 C5 N7 C N sing 1.35 N Y
9 C5 C6 C C doub 1.41 N Y
10 N3 C2 N C sing 1.32 N Y
11 C2 N1 C N doub 1.32 N Y
12 C2 H2 C H sing 1.08 N N
13 N1 C6 N C sing 1.33 N Y
14 C6 N6 C N sing 1.38 N N
15 N6 HN61 N H sing 0.97 N N
16 N6 HN62 N H sing 0.97 N N
17 C1' C2' C C sing 1.55 N N
18 C1' O4' C O sing 1.44 N N
19 C1' H1' C H sing 1.09 N N
20 C2' O2' C O sing 1.43 N N
21 C2' C3' C C sing 1.55 N N
22 C2' H2' C H sing 1.09 N N
23 O2' HO2' O H sing 0.97 N N
24 C3' O3' C O sing 1.43 N N
25 C3' C4' C C sing 1.54 N N
26 C3' H3' C H sing 1.09 N N
27 O3' P3 O P sing 1.61 N N
28 C4' O4' C O sing 1.44 N N
29 C4' C5' C C sing 1.53 N N
30 C4' H4' C H sing 1.09 N N
31 C5' O5' C O sing 1.43 N N
32 C5' H5'1 C H sing 1.09 N N
33 C5' H5'2 C H sing 1.09 N N
34 O5' P1 O P sing 1.61 N N
35 P1 O11 P O sing 1.61 N N
36 P1 O12 P O doub 1.48 N N
37 P1 O6 P O sing 1.61 N N
38 O11 HOB O H sing 0.97 N N
39 O6 P2 O P sing 1.61 N N
40 P2 O21 P O doub 1.48 N N
41 P2 O22 P O sing 1.61 N N
42 P2 O7 P O sing 1.61 N N
43 O22 HOM O H sing 0.97 N N
44 O7 CPB O C sing 1.43 N N
45 CPB CPA C C sing 1.53 N N
46 CPB HPB1 C H sing 1.09 N N
47 CPB HPB2 C H sing 1.09 N N
48 CPA CP7 C C sing 1.53 N N
49 CPA CP9 C C sing 1.53 N N
50 CPA CP8 C C sing 1.53 N N
51 CP7 OP3 C O sing 1.43 N N
52 CP7 CP6 C C sing 1.51 N N
53 CP7 H7 C H sing 1.09 N N
54 CP9 H91 C H sing 1.09 N N
55 CP9 H92 C H sing 1.09 N N
56 CP9 H93 C H sing 1.09 N N
57 CP8 H81 C H sing 1.09 N N
58 CP8 H82 C H sing 1.09 N N
59 CP8 H83 C H sing 1.09 N N
60 OP3 HO3 O H sing 0.97 N N
61 CP6 OP2 C O doub 1.21 N N
62 CP6 NP2 C N sing 1.35 N N
63 NP2 CP5 N C sing 1.46 N N
64 NP2 HN2 N H sing 0.97 N N
65 CP5 CP4 C C sing 1.53 N N
66 CP5 H51 C H sing 1.09 N N
67 CP5 H52 C H sing 1.09 N N
68 CP4 CP3 C C sing 1.51 N N
69 CP4 H41 C H sing 1.09 N N
70 CP4 H42 C H sing 1.09 N N
71 CP3 OP1 C O doub 1.21 N N
72 CP3 NP1 C N sing 1.35 N N
73 NP1 CP2 N C sing 1.47 N N
74 NP1 HN1 N H sing 0.97 N N
75 CP2 CP1 C C sing 1.53 N N
76 CP2 H21 C H sing 1.09 N N
77 CP2 H22 C H sing 1.09 N N
78 CP1 S C S sing 1.81 N N
79 CP1 H11 C H sing 1.09 N N
80 CP1 H12 C H sing 1.09 N N
81 P3 O31 P O doub 1.48 N N
82 P3 O32 P O sing 1.61 N N
83 P3 O33 P O sing 1.61 N N
84 O32 HOW O H sing 0.97 N N
85 O33 HOX O H sing 0.97 N N
86 S CS1 S C sing 1.71 N N
87 CS1 OS1 C O doub 1.21 N N
88 CS1 CS2 C C sing 1.51 N N
89 CS2 CS3 C C sing 1.53 N N
90 CS2 HS21 C H sing 1.09 N N
91 CS2 HS22 C H sing 1.09 N N
92 CS3 CS4 C C sing 1.51 N N
93 CS3 HS31 C H sing 1.09 N N
94 CS3 HS32 C H sing 1.09 N N
95 CS4 OS4 C O sing 1.34 N N
96 CS4 OS5 C O doub 1.21 N N
97 OS4 HO4 O H sing 0.97 N N



SCA : Used in PDB Entries

Total Number of PDB Entries: 10
Ligand Code PDB Entry ID Type Total Distinct
SCA 1kgt Open in New Window Bound ligand 1 1
SCA 2bwo Open in New Window Bound ligand 4 1
SCA 2vzz Open in New Window Bound ligand 4 1
SCA 3fsy Open in New Window Bound ligand 4 1
SCA 4req Open in New Window Bound ligand 2 1
SCA 5e3q Open in New Window Bound ligand 1 1
SCA 5trl Open in New Window Bound ligand 8 1
SCA 6cyj Open in New Window Bound ligand 2 1
SCA 6n2o Open in New Window Bound ligand 1 1
SCA 7d0s Open in New Window Bound ligand 1 1