Receptor
PDB id Resolution Class Description Source Keywords
5JSP 2.2 Å EC: 4.4.1.3 NEW MECHANISTIC INSIGHT FROM SUBSTRATE AND PRODUCT BOUND STR THE METAL-DEPENDENT DIMETHYLSULFONIOPROPIONATE LYASE DDDQ RUEGERIA LACUSCAERULENSIS (STRAIN DSM KCTC 2953 / ITI-1157) DIMETHYLSULFONIOPROPIONATE LYASE CUPIN METALLOENZYME
Ref.: NEW MECHANISTIC INSIGHT FROM SUBSTRATE- AND PRODUCT STRUCTURES OF THE METAL-DEPENDENT DIMETHYLSULFONIOP LYASE DDDQ. BIOCHEMISTRY V. 55 6162 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BR B:303;
A:303;
Invalid;
Invalid;
none;
none;
submit data
79.904 Br [Br-]
DQY A:302;
B:302;
Valid;
Valid;
none;
none;
submit data
136.213 C5 H12 O2 S CS(C)...
CL B:304;
B:305;
B:306;
A:304;
A:305;
A:306;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
FE A:301;
B:301;
Part of Protein;
Part of Protein;
none;
none;
submit data
55.845 Fe [Fe+3...
GOL A:307;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5JSP 2.2 Å EC: 4.4.1.3 NEW MECHANISTIC INSIGHT FROM SUBSTRATE AND PRODUCT BOUND STR THE METAL-DEPENDENT DIMETHYLSULFONIOPROPIONATE LYASE DDDQ RUEGERIA LACUSCAERULENSIS (STRAIN DSM KCTC 2953 / ITI-1157) DIMETHYLSULFONIOPROPIONATE LYASE CUPIN METALLOENZYME
Ref.: NEW MECHANISTIC INSIGHT FROM SUBSTRATE- AND PRODUCT STRUCTURES OF THE METAL-DEPENDENT DIMETHYLSULFONIOP LYASE DDDQ. BIOCHEMISTRY V. 55 6162 2016
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5JSR - AKR C3 H4 O2 C=CC(=O)O
2 5JSP - DQY C5 H12 O2 S CS(C)CCC(=....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5JSR - AKR C3 H4 O2 C=CC(=O)O
2 5JSP - DQY C5 H12 O2 S CS(C)CCC(=....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5JSR - AKR C3 H4 O2 C=CC(=O)O
2 5JSP - DQY C5 H12 O2 S CS(C)CCC(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DQY; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 DQY 1 1
2 4MV 0.44 0.666667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5JSP; Ligand: DQY; Similar sites found: 174
This union binding pocket(no: 1) in the query (biounit: 5jsp.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3WUC GLC GAL 0.009762 0.42603 None
2 2HRL SIA GAL SIA BGC NGA CEQ 0.002972 0.41157 None
3 2P7Q GG6 0.00903 0.41007 None
4 4MLO PAM 0.01224 0.41296 0.995025
5 5A65 TPP 0.01177 0.42128 1.49254
6 3OVR 5SP 0.01885 0.41273 1.49254
7 2YG2 S1P 0.002825 0.45787 1.74419
8 2YG2 FLC 0.003906 0.45541 1.74419
9 5FQ0 FLC 0.0003297 0.48173 1.75439
10 5FQK 6NT 0.002841 0.43196 1.99005
11 3OYW TDG 0.004629 0.41218 2.23881
12 1SLT NDG GAL 0.002027 0.4039 2.23881
13 1GZW GAL BGC 0.006449 0.40239 2.23881
14 1W6O LAT 0.006208 0.40229 2.23881
15 5IXH OTP 0.02127 0.42908 2.48447
16 3MPB FRU 0.00003604 0.46315 2.48756
17 2RDQ AKG 0.003566 0.44911 2.48756
18 2JIG PD2 0.0007905 0.43935 2.48756
19 2A1L PCW 0.02034 0.43426 2.48756
20 2OAZ I96 0.009179 0.42823 2.48756
21 5J75 6GQ 0.01028 0.41644 2.48756
22 2GQR ADP 0.01413 0.41186 2.48756
23 2QUN FUD 0.01352 0.41163 2.48756
24 2D6M LBT 0.00023 0.47802 2.51572
25 5C5T AKG 0.0006349 0.44294 2.63158
26 5U55 S0H 0.0228 0.40947 2.63158
27 3MTX PGT 0.0148 0.4298 2.64901
28 4IAW LIZ 0.002648 0.40769 2.65957
29 3EEB IHP 0.00582 0.43148 2.98507
30 1U0A BGC BGC BGC BGC 0.0003791 0.41211 2.98507
31 5DXT 5H5 0.01658 0.41208 2.98507
32 2FB3 GTP 0.0339 0.40643 2.98507
33 3SAO NKN 0.002727 0.43962 3.125
34 4GJY OGA 0.0001515 0.49161 3.48259
35 3W21 AKG 0.002533 0.42867 3.48259
36 4GQP B40 0.002949 0.4283 3.48259
37 4NPL AKG 0.003481 0.42582 3.48259
38 5TDF ADP 0.01249 0.42073 3.48259
39 3ETH ATP 0.01904 0.41208 3.48259
40 1ODM ASV 0.02692 0.40762 3.48259
41 4RFR RHN 0.01843 0.40539 3.48259
42 1NYW DAU 0.003478 0.44549 3.5533
43 2A4W BLM 0.003772 0.45797 3.62319
44 5FLJ QUE 0.0009501 0.47876 3.76344
45 4B7P 9UN 0.02009 0.43593 3.91304
46 1KGI T4A 0.01128 0.42709 3.93701
47 4D06 NAR 0.006406 0.43669 3.9801
48 1ZOA 140 0.02327 0.42236 3.9801
49 1I7E IBS 0.005647 0.41979 3.9801
50 4XAC AKG 0.004854 0.41883 3.9801
51 5FWJ MMK 0.003458 0.41353 3.9801
52 1ELU PDA 0.01478 0.4133 3.9801
53 1ELU CSS 0.01718 0.4133 3.9801
54 2RKV COA 0.03631 0.41025 3.9801
55 2RKV ZBA 0.04109 0.41025 3.9801
56 4OCT AKG 0.003848 0.40602 3.9801
57 5VC5 96M 0.03757 0.40331 3.9801
58 5ML3 DL3 0.02839 0.42031 4.02685
59 4K55 H6P 0.0006927 0.4588 4.03226
60 4WVW SLT 0.001066 0.45458 4.16667
61 1I82 BGC BGC 0.0004765 0.46975 4.2328
62 2XUM OGA 0.00008079 0.4899 4.47761
63 4IGQ THR M3L GLN 0.0008608 0.47682 4.47761
64 5F3I 5UJ 0.006735 0.46581 4.47761
65 3WV6 GAL BGC 0.0003601 0.4645 4.47761
66 3WV6 GAL GLC 0.0007196 0.45288 4.47761
67 3W8X FAD 0.01285 0.44659 4.47761
68 5A5W GUO 0.01164 0.44357 4.47761
69 3W8X FTK 0.003781 0.43662 4.47761
70 4Q0L V14 0.01688 0.42029 4.47761
71 4ZXA H8N 0.006268 0.40319 4.47761
72 4IGQ OGA 0.002329 0.40003 4.47761
73 1FDQ HXA 0.01642 0.42485 4.58015
74 2Z6D FMN 0.001667 0.46339 4.61538
75 1LRH NLA 0.00006354 0.47596 4.90798
76 5K21 6QF 0.01106 0.40947 4.96454
77 1Y7P RIP 0.0101 0.40371 4.97512
78 3VV1 GAL FUC 0.0003498 0.47366 5
79 4IMO PWZ 0.006109 0.41543 5.11364
80 4QM9 CYS 0.0004864 0.46833 5.20231
81 5KEW 6SB 0.002096 0.43767 5.31915
82 1N5S ADL 0.0003446 0.4204 5.35714
83 1SWG BTN 0.04156 0.40552 5.46875
84 1ZB6 GST 0.003139 0.46355 5.47264
85 1ZB6 DIN 0.002954 0.46355 5.47264
86 4OMJ 2TX 0.01633 0.42798 5.47264
87 5I0U DCY 0.000004973 0.57744 5.5
88 3WG3 A2G GAL NAG FUC 0.005748 0.41702 5.61798
89 5IXG OTP 0.04268 0.41542 5.91716
90 1GQG DCD 0.0001617 0.52279 5.97015
91 2WT2 GAL NAG GAL NAG GAL NAG 0.007001 0.43983 5.97015
92 3E8T UQ8 0.02086 0.43944 5.97015
93 3ZXE PGZ 0.001797 0.42939 5.97015
94 1ZHX HC3 0.01917 0.41616 5.97015
95 3P7N FMN 0.0001528 0.41238 5.97015
96 4AZW ATP 0.02022 0.40861 5.97015
97 1U6R ADP 0.02043 0.40613 5.97015
98 2YMZ LAT 0.0003526 0.47943 6.15385
99 3FW4 CAQ 0.009775 0.43139 6.17978
100 5DJT FMN 0.008282 0.42593 6.2069
101 3M3E GAL A2G NPO 0.002004 0.40276 6.21118
102 1WW5 SGA BGC 0.003193 0.42949 6.25
103 3NV3 GAL NAG MAN 0.0002559 0.42307 6.52174
104 1A78 TDG 0.001566 0.44568 6.71642
105 4DE9 VTP 0.002705 0.46936 6.96517
106 5DQ8 FLF 0.003251 0.45546 6.96517
107 4J25 OGA 0.001504 0.44442 6.96517
108 1LN1 DLP 0.02127 0.4231 6.96517
109 5LUN OGA 0.004983 0.41156 6.96517
110 4R38 RBF 0.004642 0.44243 7.14286
111 5DG2 GAL GLC 0.0003866 0.45495 7.40741
112 5EOB 5QQ 0.03679 0.42433 7.46269
113 3VNM SDD 0.0223 0.40164 7.46269
114 4MNS 2AX 0.01132 0.45048 7.54717
115 3PUA OGA 0.0003714 0.47495 7.9602
116 2BWA GLC BGC 0.001225 0.45768 7.9602
117 2ZMF CMP 0.004504 0.44051 7.9602
118 3AVS OGA 0.01079 0.40779 7.9602
119 1C5C TK4 0.009154 0.40628 7.9602
120 1Q8Y ADE 0.0151 0.40114 7.9602
121 5FPX GLY SER SER HIS HIS HIS HIS HIS 0.000004608 0.47016 7.9646
122 1Y0G 8PP 0.02294 0.42725 8.37696
123 5A3T MMK 0.001335 0.48397 8.45771
124 1MEX RAC 0.001523 0.45388 8.45771
125 5HV0 AKG 0.00005449 0.53205 8.95522
126 3KV5 OGA 0.001197 0.45465 8.95522
127 5EPA AKG 0.0115 0.40243 8.95522
128 4P25 FUC GAL NAG FUC 0.02652 0.40012 8.95522
129 5EPQ OLA 0.007964 0.42401 9.14634
130 5NBW 8SK 0.0008004 0.42077 9.45274
131 1MJJ HAL 0.003787 0.45418 9.69163
132 4ZU5 THM 0.005076 0.43332 9.72222
133 2YAJ 4HP 0.01782 0.40132 9.95025
134 4H6B 10Y 0.003935 0.40806 10.2564
135 4YRD 3IT 0.000006199 0.56687 10.4478
136 3HQR OGA 0.0006171 0.42557 10.4478
137 4BQY FNT 0.0001726 0.41012 10.4478
138 5L9B AKG 0.003138 0.40629 10.4478
139 5L9V OGA 0.003312 0.40339 10.4478
140 3RDO BTN 0.01135 0.41466 10.4575
141 5JNN 6LM 0.01782 0.41464 10.5263
142 2GJ3 FAD 0.02711 0.4003 10.8333
143 2FCU AKG 0.000712 0.45964 10.9453
144 1QXW M1C 0.02008 0.40551 10.9453
145 2QM9 TDZ 0.01682 0.4162 10.9677
146 2Y6Q I7T 0.02621 0.43119 11.4428
147 1SQK LAR 0.005314 0.42622 11.4428
148 3MN5 LAB 0.009136 0.40821 11.4428
149 4XIZ LPP 0.03832 0.40946 11.7647
150 3BRN SRO 0.01156 0.40242 12.7389
151 5H9Q TD2 0.0006764 0.45895 12.9032
152 5TFZ 7BC 0.0000002709 0.58744 13.3333
153 5CAD PCA 0.007948 0.40504 13.4328
154 5LDQ NAP 0.01074 0.40335 13.5593
155 4ZU4 4TG 0.0005717 0.41195 15.5405
156 5A0R ACE GLU VAL ASN PRO 0.009584 0.43472 16.1616
157 2BOS GLA GAL 0.002552 0.41345 16.1765
158 2BOS GLA GAL GLC 0.003678 0.40138 16.1765
159 4FG8 ATP 0.009837 0.42477 16.4179
160 5NFB 8VT 0.001745 0.41807 18.408
161 4M1U A2G MBG 0.001136 0.41297 18.5714
162 1J3R 6PG 0.0001374 0.4591 19.4737
163 1ERB ETR 0.001354 0.48108 19.6721
164 2GC0 PAN 0.00005213 0.44055 19.6809
165 3H9A PPY 0.0003795 0.47585 20.398
166 3H7J PPY 0.0001028 0.45174 20.398
167 4HIA FMN 0.01437 0.43525 20.398
168 5AIG VPR 0.004372 0.40741 24.8
169 1DZK PRZ 0.0008831 0.41159 24.8408
170 4QXB OGA 0.002397 0.41663 29.4118
171 3PUR 2HG 0.001594 0.44369 29.8507
172 3N9O OGA 0.003993 0.42514 29.8507
173 3N9Q OGA 0.00305 0.41897 29.8507
174 3N9P OGA 0.004445 0.41119 29.8507
Pocket No.: 2; Query (leader) PDB : 5JSP; Ligand: DQY; Similar sites found: 46
This union binding pocket(no: 2) in the query (biounit: 5jsp.bio2) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4AZP A9M 0.007399 0.43903 None
2 3KFF XBT 0.00181 0.42013 None
3 3KFF ZBT 0.00181 0.42013 None
4 2VPQ ANP 0.02304 0.40961 1.49254
5 1PZX PLM 0.02948 0.40455 1.49254
6 1Q23 FUA 0.02063 0.40521 2.48756
7 3KV4 OGA 0.006179 0.40361 2.48756
8 4FHD EEM 0.01466 0.42787 2.98507
9 4FHD 0TT 0.01466 0.42787 2.98507
10 4CSD MFU 0.007899 0.40907 2.98507
11 3ACL 3F1 0.02211 0.40286 2.98507
12 4YHO 4CC 0.02619 0.40117 2.98507
13 3R1Z ALA DGL 0.01585 0.40388 3.43008
14 2XIQ MLC 0.03606 0.40324 3.48259
15 5TPV TYD 0.008949 0.41063 3.92157
16 3E9I XAH 0.002299 0.47154 3.9801
17 3V4S ATP 0.0176 0.4121 3.9801
18 2QZ3 XYP XYP XYP 0.004122 0.44687 4.32432
19 3QRC SCR 0.007169 0.4002 4.4586
20 3ZW2 NAG GAL FUC 0.01898 0.40246 4.5977
21 2ARC ARA 0.01512 0.40241 4.87805
22 2Z93 END 0.0007249 0.40161 4.97512
23 5W10 CMP 0.01656 0.40994 6.15385
24 5J8O 6GZ 0.005189 0.43676 6.45161
25 2YKL NLD 0.0124 0.41321 6.94444
26 3A5Y KAA 0.01399 0.42171 7.46269
27 1OJK GLC BGC 0.006526 0.41867 7.46269
28 4EE7 PIS 0.00267 0.44402 7.9602
29 4YZC STU 0.01227 0.43897 7.9602
30 1Q8Y ADP 0.008766 0.42563 7.9602
31 3AVR OGA 0.003737 0.41401 7.9602
32 3ZDS HMQ 0.01017 0.4097 7.9602
33 2IXC TRH 0.02588 0.40094 7.9602
34 3L9R L9Q 0.01648 0.43291 8.16327
35 3L9R L9R 0.0316 0.41504 8.16327
36 4HN1 TYD 0.01413 0.40897 8.95522
37 4B0T ADP 0.01121 0.42693 9.45274
38 3SCM LGN 0.0276 0.4359 9.95025
39 2DIO EOD 0.01493 0.40491 11.7021
40 1ND2 MYR 0.01308 0.40901 11.9403
41 4OPC FDA 0.03895 0.442 12.4378
42 5A6N U7E 0.01968 0.40371 12.4378
43 2VDY HCY 0.01282 0.40248 12.4378
44 5H9P TD2 0.01037 0.40956 13.9241
45 5EGH PC 0.01501 0.40317 13.9303
46 3T7V MD0 0.0125 0.40223 21.393
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