Receptor
PDB id Resolution Class Description Source Keywords
4IEV 1.6 Å EC: 1.13.11.20 CYS-ONLY BOUND CYSTEINE DIOXYGENASE AT PH 8.0 IN THE PRESENC RATTUS NORVEGICUS CUPIN FOLD CATALYZES OXIDATION CYSTEINE TO CYSTEINE SULFINY157 CROSSLINK CYTOSOL OXIDOREDUCTASE
Ref.: CYSTEINE DIOXYGENASE STRUCTURES FROM PH4 TO 9: CONS CYS-PERSULFENATE FORMATION AT INTERMEDIATE PH AND A CYS-BOUND ENZYME AT HIGHER PH. J.MOL.BIOL. V. 425 3121 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FE2 A:501;
 Part of Protein;
 none;
 submit data
55.845 Fe [Fe+2...
CYS A:502;
 Valid;
 none;
 submit data
121.158 C3 H7 N O2 S C([C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5I0U 1.25 Å EC: 1.13.11.20 INCOMPLETELY INTERPRETED D-CYSTEINE SOAK OF CYSTEINE DIOXYGE 7.0 RATTUS NORVEGICUS CUPIN-FOLD CYSTEINE TO CYSTEINE SULFINATE C93-Y157 CROSSLICYSTEINE CATALYSIS OXIDATION OXIDOREDUCTASE
Ref.: STRUCTURE-BASED INSIGHTS INTO THE ROLE OF THE CYS-T CROSSLINK AND INHIBITOR RECOGNITION BY MAMMALIAN CY DIOXYGENASE. J. MOL. BIOL. V. 428 3999 2016
Members (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4XFG - CYS C3 H7 N O2 S C([C@@H](C....
2 4KWK - CSS C3 H7 N O2 S2 C([C@@H](C....
3 4IEV - CYS C3 H7 N O2 S C([C@@H](C....
4 4IES - 2CO C3 H7 N O4 S C([C@@H](C....
5 4XFH - CYS C3 H7 N O2 S C([C@@H](C....
6 4IET - 2CO C3 H7 N O4 S C([C@@H](C....
7 4XFI - HCS C4 H9 N O2 S C(CS)[C@@H....
8 4XF0 - CYS C3 H7 N O2 S C([C@@H](C....
9 3ELN - 2CO C3 H7 N O4 S C([C@@H](C....
10 4XF3 - CYS C3 H7 N O2 S C([C@@H](C....
11 4JTO - CYS C3 H7 N O2 S C([C@@H](C....
12 4IER - 2CO C3 H7 N O4 S C([C@@H](C....
13 4KWL - 3SS C3 H6 O2 S2 C(CSS)C(=O....
14 4XF1 - CYS C3 H7 N O2 S C([C@@H](C....
15 4IEW - CYS C3 H7 N O2 S C([C@@H](C....
16 4Z82 - CYS C3 H7 N O2 S C([C@@H](C....
17 5I0U - DCY C3 H7 N O2 S C([C@H](C(....
18 4PIZ - HCS C4 H9 N O2 S C(CS)[C@@H....
19 4IEY - 2CO C3 H7 N O4 S C([C@@H](C....
20 4IEU - 2CO C3 H7 N O4 S C([C@@H](C....
21 5I0R - DCY C3 H7 N O2 S C([C@H](C(....
22 4XF4 - HCS C4 H9 N O2 S C(CS)[C@@H....
23 4PIY - HCS C4 H9 N O2 S C(CS)[C@@H....
24 4XF9 - HCS C4 H9 N O2 S C(CS)[C@@H....
70% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4XFG - CYS C3 H7 N O2 S C([C@@H](C....
2 4KWK - CSS C3 H7 N O2 S2 C([C@@H](C....
3 4IEV - CYS C3 H7 N O2 S C([C@@H](C....
4 4IES - 2CO C3 H7 N O4 S C([C@@H](C....
5 4XFH - CYS C3 H7 N O2 S C([C@@H](C....
6 4IET - 2CO C3 H7 N O4 S C([C@@H](C....
7 4XFI - HCS C4 H9 N O2 S C(CS)[C@@H....
8 4XF0 - CYS C3 H7 N O2 S C([C@@H](C....
9 3ELN - 2CO C3 H7 N O4 S C([C@@H](C....
10 4XF3 - CYS C3 H7 N O2 S C([C@@H](C....
11 4JTO - CYS C3 H7 N O2 S C([C@@H](C....
12 4IER - 2CO C3 H7 N O4 S C([C@@H](C....
13 4KWL - 3SS C3 H6 O2 S2 C(CSS)C(=O....
14 4XF1 - CYS C3 H7 N O2 S C([C@@H](C....
15 4IEW - CYS C3 H7 N O2 S C([C@@H](C....
16 4Z82 - CYS C3 H7 N O2 S C([C@@H](C....
17 5I0U - DCY C3 H7 N O2 S C([C@H](C(....
18 4PIZ - HCS C4 H9 N O2 S C(CS)[C@@H....
19 4IEY - 2CO C3 H7 N O4 S C([C@@H](C....
20 4IEU - 2CO C3 H7 N O4 S C([C@@H](C....
21 5I0R - DCY C3 H7 N O2 S C([C@H](C(....
22 4XF4 - HCS C4 H9 N O2 S C(CS)[C@@H....
23 4PIY - HCS C4 H9 N O2 S C(CS)[C@@H....
24 4XF9 - HCS C4 H9 N O2 S C(CS)[C@@H....
50% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4XFG - CYS C3 H7 N O2 S C([C@@H](C....
2 4KWK - CSS C3 H7 N O2 S2 C([C@@H](C....
3 4IEV - CYS C3 H7 N O2 S C([C@@H](C....
4 4IES - 2CO C3 H7 N O4 S C([C@@H](C....
5 4XFH - CYS C3 H7 N O2 S C([C@@H](C....
6 4IET - 2CO C3 H7 N O4 S C([C@@H](C....
7 4XFI - HCS C4 H9 N O2 S C(CS)[C@@H....
8 4XF0 - CYS C3 H7 N O2 S C([C@@H](C....
9 3ELN - 2CO C3 H7 N O4 S C([C@@H](C....
10 4XF3 - CYS C3 H7 N O2 S C([C@@H](C....
11 4JTO - CYS C3 H7 N O2 S C([C@@H](C....
12 4IER - 2CO C3 H7 N O4 S C([C@@H](C....
13 4KWL - 3SS C3 H6 O2 S2 C(CSS)C(=O....
14 4XF1 - CYS C3 H7 N O2 S C([C@@H](C....
15 4IEW - CYS C3 H7 N O2 S C([C@@H](C....
16 4Z82 - CYS C3 H7 N O2 S C([C@@H](C....
17 5I0U - DCY C3 H7 N O2 S C([C@H](C(....
18 4PIZ - HCS C4 H9 N O2 S C(CS)[C@@H....
19 4IEY - 2CO C3 H7 N O4 S C([C@@H](C....
20 4IEU - 2CO C3 H7 N O4 S C([C@@H](C....
21 5I0R - DCY C3 H7 N O2 S C([C@H](C(....
22 4XF4 - HCS C4 H9 N O2 S C(CS)[C@@H....
23 4PIY - HCS C4 H9 N O2 S C(CS)[C@@H....
24 4XF9 - HCS C4 H9 N O2 S C(CS)[C@@H....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CYS; Similar ligands found: 33
No: Ligand ECFP6 Tc MDL keys Tc
1 CYS 1 1
2 DCY 1 1
3 DSN 0.65 0.84
4 SER 0.65 0.84
5 HCS 0.608696 0.916667
6 2RA 0.571429 0.807692
7 ABA 0.571429 0.75
8 DBB 0.571429 0.75
9 C2N 0.545455 0.791667
10 DAS 0.521739 0.703704
11 ASP 0.521739 0.703704
12 ASN 0.521739 0.612903
13 CSS 0.52 0.807692
14 HSE 0.5 0.75
15 DAB 0.5 0.777778
16 API 0.48 0.62069
17 AS2 0.48 0.692308
18 LEU 0.48 0.692308
19 CSO 0.48 0.677419
20 NVA 0.48 0.666667
21 GLU 0.444444 0.642857
22 DGL 0.444444 0.642857
23 GGL 0.444444 0.642857
24 DAL 0.428571 0.608696
25 ALA 0.428571 0.608696
26 ORN 0.428571 0.740741
27 NLE 0.413793 0.62069
28 3GC 0.405405 0.647059
29 DLY 0.4 0.714286
30 MED 0.4 0.666667
31 UN1 0.4 0.62069
32 11C 0.4 0.62069
33 MET 0.4 0.666667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5I0U; Ligand: DCY; Similar sites found: 131
This union binding pocket(no: 1) in the query (biounit: 5i0u.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5EPA AKG 0.0002343 0.49054 None
2 1MDC PLM 0.01278 0.41186 None
3 3SAO NKN 0.009332 0.40262 None
4 2HKA C3S 0.002059 0.4026 None
5 4OCT AKG 0.00007207 0.50116 1
6 2JIG PD2 0.00002317 0.53179 2
7 1GQG DCD 0.0001183 0.51153 2
8 3H7J PPY 0.0001134 0.47358 2
9 4WVW SLT 0.002667 0.43695 2.08333
10 5C5T AKG 0.0001005 0.50129 2.19298
11 4XCB AKG 0.001605 0.44942 2.5
12 4M26 AKG 0.00674 0.42121 2.5
13 4Y3O OGA 0.005771 0.42093 2.5
14 4MNP SLB 0.005077 0.40786 2.5
15 4D4U FUC NDG GAL FUC 0.01104 0.40543 2.5
16 1J3R 6PG 0.001391 0.44123 2.63158
17 4GJY OGA 0.000000537 0.62804 3
18 5HV0 AKG 0.000003769 0.56783 3
19 5LUN OGA 0.00006755 0.51711 3
20 3W21 AKG 0.0006515 0.46842 3
21 5KR7 6X9 0.0004382 0.4546 3
22 4MLO PAM 0.01095 0.40396 3
23 3MTX PGT 0.002979 0.45507 3.31126
24 3WG3 A2G GAL NAG FUC 0.003038 0.43759 3.37079
25 4IMO PWZ 0.004969 0.42802 3.40909
26 2HZQ STR 0.0005308 0.47687 3.44828
27 4YRD 3IT 0.000005056 0.5736 3.5
28 3AVR OGA 0.00002328 0.5437 3.5
29 3AVS OGA 0.00008062 0.49115 3.5
30 2FCU AKG 0.0007391 0.4675 3.5
31 5CAD PCA 0.001979 0.45418 3.5
32 5EOB 5QQ 0.01513 0.43702 3.5
33 4P7X YCP 0.0005276 0.43206 3.5
34 4P7X AKG 0.0005276 0.43206 3.5
35 3URB DPF 0.01066 0.41123 3.5
36 1OGX EQU 0.001962 0.41808 3.81679
37 1GG6 APL 0.01383 0.40073 3.81679
38 5T7I LAT NAG GAL 0.004972 0.42935 3.87097
39 3KV5 OGA 0.0001904 0.49513 4
40 3H9A PPY 0.0008077 0.44005 4
41 4YZC STU 0.01152 0.42982 4
42 5FYR INS 0.01079 0.41065 4
43 1ODM ASV 0.0002285 0.40581 4
44 2Z93 END 0.004633 0.4035 4
45 3KV4 OGA 0.00004453 0.52846 4.5
46 5UI2 EQ3 0.006405 0.44066 4.5
47 2IUW AKG 0.009961 0.42594 4.5
48 2IGA XXP 0.005704 0.40624 4.5
49 2IGA XX2 0.003659 0.4036 4.5
50 5FUI APY 0.006694 0.42203 4.54545
51 5TFZ 7BC 0.00006021 0.51194 4.66667
52 2ARC ARA 0.0007229 0.46027 4.87805
53 3MPB FRU 0.00004734 0.48824 5
54 5LDQ NAP 0.003892 0.43496 5.08475
55 4NS0 PIO 0.00131 0.45222 5.26316
56 1I82 BGC BGC 0.007501 0.41808 5.29101
57 5BVB DOG 0.01329 0.4058 5.30303
58 1N5S ADL 0.002267 0.40903 5.35714
59 5JSP DQY 0.000004973 0.57744 5.5
60 3PUA OGA 0.00000698 0.57003 5.5
61 1OIJ AKG 0.002756 0.43753 5.5
62 5FQK 6NT 0.004996 0.42789 5.5
63 2XN5 FUN 0.006775 0.40912 5.5
64 4YLZ LAT NAG GAL 0.003943 0.43463 5.88235
65 4B1M FRU FRU 0.0008661 0.41446 5.94595
66 4NPL AKG 0.00005553 0.47677 6
67 1O4T OXL 0.0101 0.40874 6.01504
68 5FPX GLY SER SER HIS HIS HIS HIS HIS 0.000004154 0.49979 6.19469
69 3A16 PXO 0.01 0.40889 6.5
70 4IAW LIZ 0.01186 0.40201 6.91489
71 4XAC AKG 0.00009366 0.514 7
72 5L9V OGA 0.0001813 0.48249 7
73 5L9B AKG 0.0001859 0.48198 7
74 4IGQ THR M3L GLN 0.0003905 0.47982 7
75 3HQR OGA 0.0001743 0.47389 7
76 4JZR 4JR 0.0008513 0.45687 7
77 5C3R HMU 0.0001054 0.45271 7
78 5C3R AKG 0.0001054 0.45271 7
79 4BQY FNT 0.00005753 0.44995 7
80 4IGQ OGA 0.000027 0.44152 7
81 4RFR RHN 0.001047 0.41289 7
82 3N9Q OGA 0.0002061 0.49158 7.5
83 3N9P OGA 0.0002343 0.48929 7.5
84 3N9O OGA 0.0002445 0.48791 7.5
85 4N14 WR7 0.001 0.46649 7.5
86 3PUR 2HG 0.003035 0.43784 7.5
87 5VE5 GSH 0.01866 0.40039 7.5
88 5FU3 BGC BGC BGC 0.000573 0.47408 7.54717
89 1BHX ASP PHE GLU GLU ILE 0.005629 0.41289 7.61905
90 4ZU5 THM 0.004527 0.42439 7.63889
91 5F3I 5UJ 0.0003172 0.52755 8
92 2Q8C AKG 0.00007213 0.52182 8
93 5FWE OGA 0.0000939 0.51537 8
94 5LY2 OGA 0.0001117 0.51108 8
95 2Q8E OGA 0.000127 0.50783 8
96 2OS2 OGA 0.000188 0.49913 8
97 2YBP 2HG 0.0002384 0.49382 8
98 2P5B OGA 0.0003317 0.46021 8
99 1I7E IBS 0.003514 0.43962 8
100 3JRS A8S 0.01475 0.40717 8
101 2OVD DAO 0.008564 0.41627 8.24176
102 1MEX RAC 0.008615 0.40424 8.5
103 1EPB REA 0.001128 0.42003 8.53659
104 1LRH NLA 0.00003684 0.51474 8.58896
105 5FWJ MMK 0.0002584 0.48166 9
106 3A6T 8OG 0.004703 0.40001 9.30233
107 2D6M LBT 0.009754 0.40058 9.43396
108 5FP3 3JI 0.0001194 0.42367 9.5
109 4J25 OGA 0.0004209 0.47961 9.60699
110 2XUM OGA 0.0000009451 0.61347 10
111 2NSX IFM 0.006168 0.40589 10
112 4ZXA H8N 0.001519 0.44483 10.5
113 3ZDS HQ9 0.006855 0.41997 11
114 1SR7 MOF 0.02072 0.41225 11
115 3ZDS OMD 0.01138 0.40288 11
116 3ZDS HMQ 0.009252 0.40279 11
117 4UF0 MMK 0.01048 0.40263 11.5
118 5UQD AKG 0.0001865 0.50284 12
119 2A4W BLM 0.02214 0.40712 12.3188
120 5FLJ QUE 0.000578 0.41327 13.9785
121 4QXB OGA 0.00009526 0.5024 14
122 5OO5 UUA 0.0001941 0.4512 14.5161
123 1Y0G 8PP 0.04447 0.40484 15.1832
124 4MA6 28E 0.009382 0.41161 15.2866
125 2OG7 SIN 0.008132 0.40977 16
126 5VNF VAL THR SER VAL VAL 0.01123 0.40316 17.1975
127 3OPT AKG 0.0001613 0.50217 18.5
128 3KFF ZBT 0.01456 0.40217 20.3704
129 3KFF XBT 0.01456 0.40217 20.3704
130 2GC0 PAN 0.00125 0.41985 27.1277
131 4BXF AKG 0.002409 0.44245 31.5789
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