Receptor
PDB id Resolution Class Description Source Keywords
4IZD 1.8 Å EC: 5.-.-.- CRYSTAL STRUCTURE OF DMDD E121A IN COMPLEX WITH MMPA-COA RUEGERIA POMEROYI ENOYL-COA HYDRATASE HYDROLASE DIMETHYL-SULPHONIOPROPIONATEMETABOLISM METHYLTHIOACRYLOYL-COA (MTA-COA) CROTONASE FOLHYDROLASE-SUBSTRATE COMPLEX
Ref.: CRYSTAL STRUCTURE OF DMDD, A CROTONASE SUPERFAMILY THAT CATALYZES THE HYDRATION AND HYDROLYSIS OF METHYLTHIOACRYLOYL-COA. PLOS ONE V. 8 63870 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
1HE B:301;
A:301;
Valid;
Valid;
none;
none;
submit data
869.689 C25 H42 N7 O17 P3 S2 CC(C)...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4IZC 1.8 Å EC: 5.-.-.- CRYSTAL STRUCTURE OF DMDD E121A IN COMPLEX WITH MTA-COA RUEGERIA POMEROYI ENOYL-COA HYDRATASE HYDROLASEMETHYLTHIOACRYLOYL-COA (MTA-CDIMETHYL-SULPHONIOPROPIONATE (DMSP) METABOLISM CROTONASE FENYOL-COA HYDRATASE HYDROLASE HYDROLASE-HYDROLASE INHIBITCOMPLEX HYDROLASE-SUBSTRATE COMPLEX
Ref.: CRYSTAL STRUCTURE OF DMDD, A CROTONASE SUPERFAMILY THAT CATALYZES THE HYDRATION AND HYDROLYSIS OF METHYLTHIOACRYLOYL-COA. PLOS ONE V. 8 63870 2013
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 4IZC - 1GZ C25 H40 N7 O17 P3 S2 CC(C)(COP(....
2 4IZD - 1HE C25 H42 N7 O17 P3 S2 CC(C)(COP(....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 24 families.
1 4IZC - 1GZ C25 H40 N7 O17 P3 S2 CC(C)(COP(....
2 4IZD - 1HE C25 H42 N7 O17 P3 S2 CC(C)(COP(....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 4IZC - 1GZ C25 H40 N7 O17 P3 S2 CC(C)(COP(....
2 4IZD - 1HE C25 H42 N7 O17 P3 S2 CC(C)(COP(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 1HE; Similar ligands found: 143
No: Ligand ECFP6 Tc MDL keys Tc
1 1HE 1 1
2 BCO 0.904 0.955556
3 SCA 0.889764 0.955556
4 1VU 0.888 0.945055
5 OXK 0.88 0.955556
6 3HC 0.874016 0.966292
7 MLC 0.874016 0.955556
8 IVC 0.874016 0.966292
9 ACO 0.870968 0.966667
10 GRA 0.869231 0.955556
11 HXC 0.869231 0.956044
12 CAA 0.867188 0.966292
13 3KK 0.857143 0.955556
14 CO8 0.856061 0.956044
15 CAO 0.854839 0.923913
16 COS 0.854839 0.934066
17 HGG 0.853846 0.955556
18 5F9 0.849624 0.956044
19 MYA 0.849624 0.956044
20 MFK 0.849624 0.956044
21 UCC 0.849624 0.956044
22 DCC 0.849624 0.956044
23 ST9 0.849624 0.956044
24 FAQ 0.847328 0.955556
25 CO6 0.84375 0.955556
26 2MC 0.837209 0.914894
27 TGC 0.834586 0.966667
28 FYN 0.828125 0.955056
29 1GZ 0.825758 0.966667
30 MCA 0.824427 0.945055
31 COO 0.824427 0.955556
32 SOP 0.821705 0.955556
33 COK 0.821705 0.934066
34 YNC 0.818841 0.945055
35 MC4 0.818182 0.905263
36 COA 0.816 0.955056
37 0T1 0.816 0.933333
38 CMC 0.815385 0.955556
39 DCA 0.814516 0.912088
40 COW 0.81203 0.945055
41 IRC 0.81203 0.966292
42 BYC 0.81203 0.955556
43 COF 0.81203 0.934783
44 30N 0.811024 0.876289
45 CS8 0.810219 0.967033
46 BCA 0.80597 0.945055
47 HDC 0.804348 0.956044
48 A1S 0.80303 0.977528
49 ETB 0.8 0.922222
50 AMX 0.796875 0.94382
51 2CP 0.791045 0.945055
52 CMX 0.790698 0.933333
53 SCO 0.790698 0.933333
54 1CZ 0.788321 0.945055
55 2NE 0.788321 0.934783
56 3CP 0.785185 0.955556
57 2KQ 0.785185 0.956044
58 FCX 0.784615 0.903226
59 FAM 0.784615 0.913043
60 4CA 0.779412 0.945055
61 HAX 0.778626 0.913043
62 CIC 0.775362 0.955556
63 WCA 0.771429 0.934783
64 SCD 0.768657 0.933333
65 CAJ 0.768657 0.913043
66 CA6 0.766917 0.907216
67 MCD 0.766917 0.934066
68 4KX 0.765957 0.924731
69 NMX 0.761194 0.865979
70 MRS 0.760563 0.956044
71 MRR 0.760563 0.956044
72 4CO 0.757143 0.945055
73 0FQ 0.757143 0.955556
74 DAK 0.755245 0.967033
75 0ET 0.751773 0.956044
76 01A 0.751773 0.914894
77 8Z2 0.75 0.945652
78 CCQ 0.75 0.956522
79 1CV 0.746479 0.955556
80 YE1 0.744526 0.923077
81 UOQ 0.741259 0.956044
82 NHM 0.741259 0.956044
83 NHW 0.741259 0.956044
84 UCA 0.738562 0.956044
85 HFQ 0.736111 0.934783
86 CA8 0.733813 0.868687
87 1HA 0.72973 0.934783
88 NHQ 0.727891 0.966292
89 S0N 0.725352 0.913043
90 01K 0.713333 0.955556
91 COT 0.708609 0.955556
92 CA3 0.688312 0.955556
93 CO7 0.683099 0.955556
94 CA5 0.677215 0.914894
95 93P 0.6625 0.945055
96 COD 0.661654 0.94382
97 93M 0.652439 0.945055
98 COA PLM 0.646667 0.923913
99 COA MYR 0.646667 0.923913
100 PLM COA 0.646667 0.923913
101 HMG 0.633333 0.923077
102 4BN 0.624277 0.915789
103 5TW 0.624277 0.915789
104 JBT 0.615819 0.896907
105 OXT 0.612717 0.915789
106 BSJ 0.582857 0.924731
107 191 0.551948 0.85
108 PAP 0.54918 0.775281
109 SFC 0.512048 0.934783
110 RFC 0.512048 0.934783
111 PPS 0.511811 0.721649
112 A3P 0.5 0.764045
113 ACE SER ASP ALY THR NH2 COA 0.497355 0.913043
114 0WD 0.493243 0.755319
115 PTJ 0.442857 0.833333
116 PUA 0.43949 0.784946
117 3AM 0.439024 0.752809
118 PAJ 0.434783 0.844444
119 A22 0.430657 0.777778
120 A2D 0.425197 0.766667
121 ME8 0.422535 0.866667
122 3OD 0.422535 0.788889
123 SAP 0.421053 0.791209
124 AGS 0.421053 0.791209
125 ATR 0.421053 0.764045
126 NA7 0.41844 0.820225
127 ADP 0.415385 0.786517
128 ADQ 0.414286 0.769231
129 A2R 0.413043 0.777778
130 APU 0.411765 0.752688
131 AD9 0.410448 0.769231
132 OAD 0.408451 0.788889
133 BA3 0.407692 0.766667
134 ATP 0.406015 0.786517
135 B4P 0.40458 0.766667
136 AP5 0.40458 0.766667
137 48N 0.403974 0.774194
138 APR 0.402985 0.766667
139 AQP 0.402985 0.786517
140 AR6 0.402985 0.766667
141 5FA 0.402985 0.786517
142 2A5 0.402985 0.808989
143 AN2 0.401515 0.777778
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4IZC; Ligand: 1GZ; Similar sites found: 206
This union binding pocket(no: 1) in the query (biounit: 4izc.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.02589 0.45682 None
2 1TUV VK3 0.01901 0.44929 None
3 3RF4 FUN 0.01733 0.42367 None
4 3BY8 MLT 0.04496 0.41746 None
5 2E1A MSE 0.02693 0.41063 None
6 2IF8 ADP 0.03568 0.40884 1.45455
7 1K27 MTM 0.0008634 0.40845 1.45455
8 1MVQ MMA 0.001237 0.40643 1.69492
9 3LTW HLZ 0.009741 0.44579 1.81818
10 1Z44 NPO 0.0406 0.44496 1.81818
11 4N9Z V3L 0.01579 0.43669 1.81818
12 1V6A TRE 0.03392 0.41425 1.81818
13 1Z48 FMN 0.01389 0.40835 1.81818
14 1Z41 FMN 0.01473 0.40731 1.81818
15 1G6H ADP 0.02801 0.41071 1.94553
16 1NU4 MLA 0.005374 0.4423 2.06186
17 3ZPG 5GP 0.003327 0.49097 2.18182
18 2F2U M77 0.007598 0.43101 2.18182
19 1NJR XYL 0.002424 0.40541 2.18182
20 2D2I NAP 0.004843 0.40377 2.18182
21 2WCI GSH 0.02056 0.42477 2.22222
22 3NOJ PYR 0.0001634 0.5213 2.52101
23 1TV5 A26 0.00006138 0.47772 2.54545
24 3TFC PEP 0.004475 0.45102 2.54545
25 1TV5 ORO 0.001571 0.44451 2.54545
26 4PB2 5UD 0.002952 0.4278 2.54545
27 4JWX 1N4 0.01538 0.4261 2.54545
28 2JFV FLC 0.03464 0.41838 2.54545
29 1TV5 N8E 0.005311 0.41798 2.54545
30 2C5S AMP 0.02887 0.40925 2.54545
31 3MD0 GDP 0.02933 0.40894 2.54545
32 3MAG SAH 0.01074 0.40306 2.54545
33 3TKA SAM 0.01055 0.40036 2.54545
34 1MZV AMP 0.006253 0.43471 2.55319
35 1G8S MET 0.001684 0.48343 2.6087
36 3LQV ADE 0.002993 0.44804 2.6087
37 4OHB 5HM 0.004088 0.42988 2.63158
38 1S8F GDP 0.002978 0.40526 2.82486
39 1PEA ACM 0.0234 0.43792 2.85714
40 4MOB ADP 0.000894 0.45427 2.90909
41 1GJW GLC 0.01402 0.44359 2.90909
42 3O2K QRP 0.004742 0.43998 2.90909
43 2GN2 C5P 0.004 0.4264 2.90909
44 1H0C AOA 0.04157 0.41924 2.90909
45 1SQ5 ADP 0.01277 0.41713 2.90909
46 4L8F MTX 0.03421 0.41259 2.90909
47 4MOB COA 0.0002232 0.40925 2.90909
48 1E5F PLP 0.01968 0.40219 2.90909
49 1XE7 GUN 0.03496 0.43459 2.95567
50 1QO0 BMD 0.01646 0.4345 3.06122
51 3KJQ B94 0.003671 0.44024 3.15789
52 2Y7P SAL 0.008146 0.43894 3.21101
53 2QV7 ADP 0.000108 0.49363 3.27273
54 1A5Z OXM 0.004417 0.47635 3.27273
55 2Q1A 2KT 0.00008849 0.47203 3.27273
56 2ZO9 MLI 0.001229 0.46301 3.27273
57 1A5Z FBP 0.0009767 0.44222 3.27273
58 4WVH ASP HIS ASP ALA HIS ALA 0.006058 0.43996 3.27273
59 1YBQ BDH 0.0002015 0.41847 3.27273
60 1KTC NGA 0.02422 0.41688 3.27273
61 3BRE C2E 0.04075 0.41484 3.27273
62 1ONX ASP 0.002019 0.41081 3.27273
63 1CKM GTP 0.03633 0.4047 3.27273
64 3UEC ALA ARG TPO LYS 0.01466 0.44261 3.42466
65 1YQC GLV 0.004336 0.44396 3.52941
66 2O2C G6Q 0.001537 0.44705 3.63636
67 5DRN 5CT 0.0376 0.43605 3.63636
68 1T10 F6P 0.0143 0.43236 3.63636
69 3PLN U5P 0.01461 0.42713 3.63636
70 2BH9 NAP 0.007072 0.42025 3.63636
71 4CIB 7UZ 0.03407 0.41297 3.63636
72 4IMG NGF 0.01155 0.40186 3.63636
73 1A8S PPI 0.0000637 0.51842 3.663
74 3KMZ EQO 0.003104 0.40467 3.7594
75 3F81 STT 0.0003594 0.54399 3.82514
76 3BHO B4P 0.01045 0.47156 3.84615
77 2Y6P CTP 0.03477 0.40188 3.84615
78 4L6C 0BT 0.007257 0.40336 3.9604
79 3NGU ADP 0.0005856 0.46893 3.97351
80 2YP9 SIA CMO 0.0004672 0.46551 4
81 4KCT PYR 0.01374 0.42389 4
82 3QV9 QV7 0.04473 0.40841 4
83 2Z5Y HRM 0.002543 0.40205 4
84 2B7N NTM 0.01031 0.43918 4.0293
85 1J2Z SOG 0.0003795 0.46912 4.07407
86 3K56 IS3 0.02504 0.40213 4.13534
87 1B4P GPS 0.008523 0.41006 4.14747
88 1SJW NGV 0.0119 0.41108 4.16667
89 1XIU REA 0.003254 0.42993 4.34783
90 4RJK PYR 0.01711 0.46767 4.36364
91 4M5P MLA 0.02311 0.45171 4.36364
92 2NVK NAP 0.007153 0.44156 4.36364
93 4M5P 23W 0.0217 0.43966 4.36364
94 1BGV GLU 0.03108 0.41349 4.36364
95 1V8K ANP 0.001196 0.40687 4.36364
96 3I8P 840 0.01674 0.40505 4.36364
97 4P4T GDP 0.01339 0.40247 4.36364
98 1WKL ATP 0.0001122 0.48241 4.37956
99 1WKL ADP 0.001226 0.44248 4.37956
100 1YOA FMN 0.004527 0.5023 4.40252
101 1YOA FAD 0.004695 0.41016 4.40252
102 1WHT BZS 0.01711 0.43198 4.57516
103 1ULE GLA GAL NAG 0.0263 0.42437 4.66667
104 4M51 BEZ 0.01724 0.445 4.72727
105 1ON3 MCA 0.0005146 0.40639 4.72727
106 3CF6 SP1 0.02075 0.40125 4.72727
107 1H65 GDP 0.01039 0.40061 4.81482
108 3QDT A2G GAL 0.007988 0.46273 4.8951
109 3QDY A2G GAL 0.009585 0.45854 4.8951
110 3QDY CBS 0.0251 0.43058 4.8951
111 1FNZ A2G 0.001012 0.43408 5.06329
112 4E28 9MZ 0.04323 0.41355 5.09091
113 2X1L MET 0.04009 0.40581 5.09091
114 2HK9 ATR 0.03339 0.40274 5.09091
115 2Q1W NAD 0.001557 0.40084 5.09091
116 1SS4 GSH 0.003281 0.51743 5.22876
117 1SS4 CIT 0.002827 0.47332 5.22876
118 1RZM E4P 0.0271 0.42887 5.45455
119 4Q3S X7A 0.0007944 0.42256 5.45455
120 2GJN FMN 0.002417 0.41114 5.45455
121 2GJN NIS 0.002385 0.40563 5.45455
122 1VCO GLN 0.003029 0.40502 5.45455
123 1ECM TSA 0.02507 0.41205 5.50459
124 4F8L GAL 0.00672 0.49203 5.51724
125 4FUA PGH 0.001118 0.41925 5.5814
126 2ZL4 ALA ALA ALA ALA 0.0409 0.40561 5.61225
127 3E5H GNP 0.005442 0.40203 5.61798
128 4K30 NLG 0.02216 0.41868 5.625
129 1Y9Q MED 0.02616 0.42448 5.72917
130 2ZWS PLM 0.01642 0.46875 5.81818
131 2C9O ADP 0.0004702 0.41629 5.81818
132 3I0O SMI 0.04306 0.40921 5.81818
133 3I0O ADP 0.03594 0.40124 5.81818
134 2WLT ASP 0.002887 0.40031 5.81818
135 2HNK SAH 0.0118 0.40152 5.85774
136 3KPE TM3 0.01984 0.43046 5.88235
137 4IXW IXW 0.01907 0.41745 5.90551
138 1Y75 NAG 0.01895 0.41757 5.9322
139 2JGS BTN 0.005054 0.45123 6.15385
140 4IEN COA 0.00002775 0.45278 6.18182
141 4QDF 30Q 0.002655 0.4055 6.18182
142 4IEN GDP 0.003245 0.40267 6.18182
143 1NVV GNP 0.00454 0.40193 6.18182
144 3DGY 2GP 0.02909 0.41513 6.18557
145 2EB5 OXL 0.01757 0.43309 6.36704
146 2PVQ GSH 0.008478 0.41351 6.46766
147 2QLX RM4 0.03903 0.42066 6.48148
148 1FX8 BOG 0.000878 0.45236 6.54545
149 1Z82 G3H 0.04813 0.40176 6.54545
150 1GXU 2HP 0.004302 0.41152 6.59341
151 1EJE FMN 0.009232 0.40872 6.77083
152 3R51 MMA 0.003963 0.48679 6.875
153 2IZ1 ATR 0.008249 0.44937 6.90909
154 4BCQ TJF 0.02307 0.41492 6.90909
155 2ZJ5 ADP 0.01781 0.42777 7.27273
156 1W7J ADP BEF 0.00645 0.4182 7.28477
157 4K4D HFQ 0.0059 0.41831 7.29927
158 1EB9 HBA 0.01454 0.41471 7.63359
159 1JQN DCO 0.0003354 0.41777 7.63636
160 4RLE 2BA 0.0009263 0.40754 7.69231
161 4F4S EFO 0.00316 0.45802 7.89474
162 4CCO OGA 0.004555 0.45066 8
163 2JBH 5GP 0.01846 0.41809 8
164 2Z9V PXM 0.03063 0.41209 8
165 2BII MTV 0.003686 0.41083 8
166 2IYG FMN 0.009846 0.42196 8.06452
167 2FR6 URI 0.005382 0.41776 8.21918
168 2Y7G AAE 0.01436 0.40776 8.36364
169 1QZZ SAM 0.02512 0.4011 8.36364
170 2DPY ADP 0.04244 0.40474 8.72727
171 3P7I P7I 0.003463 0.45618 9.09091
172 3H0L ADP 0.02108 0.41698 9.09091
173 1ZJ6 G3D 0.004024 0.43853 9.45455
174 1QDS PGA 0.01534 0.4176 9.96016
175 3SHR CMP 0.004104 0.44273 10.0334
176 2O66 FLC 0.004483 0.4565 10.3704
177 3VOZ 04A 0.001798 0.44009 10.9091
178 3VGL BGC 0.0006025 0.42179 10.9091
179 1QD0 RR6 0.01273 0.41718 10.9375
180 4HE2 AMP 0.0008342 0.41162 11.2727
181 1FWY UD1 0.000639 0.41233 11.6364
182 3A2Y TS5 0.003628 0.42807 11.6751
183 1F1V DHY 0.004295 0.44669 12
184 2YCD GTB 0.02696 0.4032 12.1739
185 2WMO GTP 0.004881 0.43075 12.6316
186 3VSV XYP 0.04277 0.40074 12.7273
187 3D3H M4O 0.02164 0.40051 14
188 2YLD CMO 0.00681 0.45348 14.1732
189 1RN8 DUP 0.002285 0.41653 14.4737
190 3DG6 MUC 0.02312 0.40261 14.5455
191 2PP3 LGT 0.002519 0.40625 14.9091
192 3A1I UNU 0.002967 0.44889 15.6364
193 2Q37 3AL 0.001621 0.47761 18.232
194 1RGE 2GP 0.02856 0.41557 20.8333
195 2A2X NA9 0.007108 0.4131 26.4706
196 2FYU FDN 0.01326 0.40264 27.2727
197 1SG4 CO8 0.000003808 0.52843 27.3077
198 1XX4 BAM 0.00266 0.46436 29.5019
199 4QIJ 1HA 0.00001013 0.53716 29.8182
200 2NP9 YE1 0.0000000002957 0.60042 33.8182
201 4I42 1HA 0.000003771 0.54083 34.9091
202 1DUB CAA 0.0000004242 0.41624 35.6322
203 4I4Z 2NE 0.000002213 0.5283 36
204 2VSS ACO 0.000000001302 0.53607 36.7273
205 1JXZ BCA 0.0000002653 0.52975 37.9182
206 1NZY BCA 0.0000003216 0.52656 38.29
Pocket No.: 2; Query (leader) PDB : 4IZC; Ligand: 1GZ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4izc.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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