Receptor
PDB id Resolution Class Description Source Keywords
1Q7E 1.6 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF YFDW PROTEIN FROM E. COLI ESCHERICHIA COLI STRUCTURAL GENOMICS INTERTWINED DIMER PSI PROTEIN STRUCTUINITIATIVE NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENNYSGXRC TRANSFERASE
Ref.: STRUCTURE OF ESCHERICHIA COLI YFDW, A TYPE III COA TRANSFERASE. ACTA CRYSTALLOGR.,SECT.D V. 60 507 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MET A:500;
A:600;
Valid;
Valid;
none;
none;
submit data
149.211 C5 H11 N O2 S CSCC[...
MPD A:1000;
A:1100;
A:1200;
A:1300;
A:700;
A:800;
A:900;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
118.174 C6 H14 O2 C[C@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1Q7E 1.6 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF YFDW PROTEIN FROM E. COLI ESCHERICHIA COLI STRUCTURAL GENOMICS INTERTWINED DIMER PSI PROTEIN STRUCTUINITIATIVE NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENNYSGXRC TRANSFERASE
Ref.: STRUCTURE OF ESCHERICHIA COLI YFDW, A TYPE III COA TRANSFERASE. ACTA CRYSTALLOGR.,SECT.D V. 60 507 2004
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 236 families.
1 1PT8 - OXL C2 O4 C(=O)(C(=O....
2 1PT5 - ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
3 1Q7E - MET C5 H11 N O2 S CSCC[C@@H]....
4 1Q6Y - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
70% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 211 families.
1 1PT8 - OXL C2 O4 C(=O)(C(=O....
2 1PT5 - ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
3 1Q7E - MET C5 H11 N O2 S CSCC[C@@H]....
4 1Q6Y - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
5 1P5R - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
6 1T3Z - CAO C21 H36 N7 O17 P3 S CC(C)(CO[P....
7 1VGR - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
8 2VJO - OXL C2 O4 C(=O)(C(=O....
9 1VGQ - CAO C21 H36 N7 O17 P3 S CC(C)(CO[P....
10 3UBM - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 166 families.
1 1PT8 - OXL C2 O4 C(=O)(C(=O....
2 1PT5 - ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
3 1Q7E - MET C5 H11 N O2 S CSCC[C@@H]....
4 1Q6Y - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
5 1P5R - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
6 1T3Z - CAO C21 H36 N7 O17 P3 S CC(C)(CO[P....
7 1VGR - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
8 2VJO - OXL C2 O4 C(=O)(C(=O....
9 1VGQ - CAO C21 H36 N7 O17 P3 S CC(C)(CO[P....
10 3UBM - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MET; Similar ligands found: 32
No: Ligand ECFP6 Tc MDL keys Tc
1 MET 1 1
2 MED 1 1
3 DBB 0.518519 0.655172
4 ABA 0.518519 0.655172
5 2FM 0.514286 0.666667
6 NVA 0.5 0.758621
7 MF3 0.5 0.647059
8 DAB 0.466667 0.636364
9 HSE 0.466667 0.617647
10 SME 0.457143 0.717949
11 MHO 0.457143 0.717949
12 HCS 0.451613 0.733333
13 API 0.451613 0.606061
14 CDT 0.447368 0.756757
15 2MM 0.444444 0.657143
16 NLE 0.441176 0.766667
17 ONL 0.441176 0.71875
18 UN1 0.428571 0.606061
19 11C 0.428571 0.606061
20 MSE 0.428571 0.9
21 GGL 0.424242 0.625
22 GLU 0.424242 0.625
23 DGL 0.424242 0.625
24 CBH 0.418605 0.685714
25 ORN 0.411765 0.65625
26 AME 0.410256 0.771429
27 FME 0.410256 0.84375
28 LEU 0.40625 0.666667
29 CYS 0.4 0.666667
30 C2N 0.4 0.633333
31 DCY 0.4 0.666667
32 JM6 0.4 0.7
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1Q7E; Ligand: MET; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1q7e.bio1) has 6 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1Q7E; Ligand: MET; Similar sites found: 195
This union binding pocket(no: 2) in the query (biounit: 1q7e.bio1) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.001844 0.50086 None
2 3RF4 FUN 0.006515 0.4205 None
3 4FR3 LYS ARG ARG LYS SEP VAL 0.007896 0.40335 None
4 3Q3C NAD 0.001702 0.4154 1.00334
5 9LDB NAD 0.0003492 0.41511 1.20482
6 9LDT NAD 0.0003512 0.41503 1.20482
7 4E28 0MZ 0.005251 0.42996 1.23077
8 4E28 9MZ 0.007409 0.42891 1.23077
9 1V6A TRE 0.004239 0.43409 1.50602
10 1SOW NAD 0.0001048 0.43254 1.52439
11 2FOI JPA 0.005811 0.413 1.85874
12 4KCT FDP 0.0003109 0.45857 1.86916
13 2XDQ MGX 0.01036 0.44157 1.86916
14 3QV9 QV7 0.00321 0.43947 1.86916
15 4KCT PYR 0.003677 0.42596 1.86916
16 3T31 FAD 0.00101 0.42462 1.86916
17 3T31 DCQ 0.001129 0.42462 1.86916
18 3RO7 TDR 0.01651 0.40211 1.88679
19 3JQ3 ADP 0.00884 0.40561 1.91257
20 1L5Y BEF 0.02289 0.40273 1.93548
21 1SS4 CIT 0.00002544 0.6384 1.96078
22 1SS4 GSH 0.003249 0.4972 1.96078
23 2F2U M77 0.002987 0.4247 1.99005
24 2Z9V PXM 0.002483 0.43855 2.04082
25 3NFZ 3NF 0.005837 0.40854 2.14067
26 1KYQ NAD 0.0006303 0.42731 2.18978
27 2Q8H TF4 0.01194 0.43836 2.2113
28 3ITA AIC 0.01135 0.42763 2.27273
29 3WBF API 0.001196 0.40157 2.29508
30 1T26 GBD 0.0007288 0.45064 2.33645
31 1T26 NAI 0.0007288 0.45064 2.33645
32 1A8S PPI 0.002381 0.42624 2.33645
33 1GV0 NAD 0.0003577 0.41328 2.33645
34 3GJB AKG 0.009498 0.40874 2.33645
35 3D3H M4O 0.003785 0.40751 2.33645
36 2C7G FAD 0.003544 0.40718 2.33645
37 2IMP NAI 0.01069 0.40265 2.33645
38 3MPI GRA 0.004928 0.40085 2.33645
39 2C7G ODP 0.00528 0.40062 2.33645
40 3PLN U5P 0.009124 0.41419 2.35849
41 2YLD CMO 0.001846 0.45671 2.3622
42 4M5P MLA 0.003383 0.47573 2.457
43 4M5P 23W 0.007294 0.44204 2.457
44 4PPU TYR 0.01525 0.40454 2.51799
45 2G86 UMP 0.003123 0.40415 2.53165
46 3MD0 GDP 0.005174 0.41976 2.53521
47 1HYE NAP 0.0006439 0.41117 2.55591
48 2Y6P CTP 0.009798 0.40379 2.5641
49 2IZ1 ATR 0.005096 0.4364 2.57009
50 3GTD MLI 0.009945 0.41759 2.57009
51 4M51 BEZ 0.0008756 0.48768 2.57611
52 3MAG 3MA 0.03103 0.4236 2.60586
53 1RM4 NDP 0.005609 0.40264 2.67062
54 3OCZ SRA 0.004728 0.40012 2.67176
55 1GU3 BGC BGC BGC BGC BGC 0.01139 0.41003 2.68456
56 3F81 STT 0.0003327 0.51864 2.73224
57 1KYZ SAH 0.0025 0.40626 2.73973
58 2Q37 3AL 0.005003 0.43089 2.76243
59 4W6Z 8ID 0.0003123 0.42353 2.80374
60 3CQ5 PMP 0.004619 0.42182 2.80374
61 3ZPG 5GP 0.004576 0.45991 2.87958
62 2WGC SIA GAL BGC 0.01834 0.44439 2.92398
63 1WGC SIA GAL BGC 0.03506 0.4207 2.92398
64 1XE7 GUN 0.01666 0.43085 2.95567
65 1KTC NGA 0.0005759 0.46586 2.96296
66 2EB5 OXL 0.006041 0.433 2.99625
67 2PP3 LGT 0.003975 0.4108 3.01508
68 4RJK PYR 0.0001081 0.57037 3.03738
69 2NCD ADP 0.0009002 0.46402 3.09524
70 1RYD GLC 0.02862 0.4083 3.10078
71 3TFC PEP 0.01257 0.40817 3.11688
72 3R51 MMA 0.001423 0.4861 3.125
73 1Y9Q MED 0.02266 0.40643 3.125
74 1UPR 4IP 0.01483 0.43916 3.25203
75 2QV7 ADP 0.001862 0.41895 3.2641
76 3R4S SLB 0.006652 0.45855 3.27103
77 1T10 F6P 0.02184 0.40229 3.27103
78 1KGQ SCO 0.008995 0.40422 3.28467
79 3NOJ PYR 0.01048 0.41403 3.36134
80 1Q11 TYE 0.0006446 0.46375 3.49462
81 4C6F DOR 0.007579 0.40832 3.56234
82 4C6F NCD 0.007579 0.40832 3.56234
83 3LTW HLZ 0.002339 0.45198 3.57143
84 3SHR CMP 0.005673 0.41342 3.67893
85 4OHB 5HM 0.001021 0.42864 3.68421
86 2QLX RM4 0.02685 0.40816 3.7037
87 3TKA CTN 0.02613 0.41947 3.7464
88 1TDF NAP 0.001199 0.43239 3.79747
89 1TDF FAD 0.003051 0.40273 3.79747
90 1QO0 BMD 0.002638 0.44958 3.8961
91 1PEA ACM 0.02313 0.41706 3.8961
92 3AB4 LYS 0.01112 0.40936 3.93258
93 1CKM GTP 0.006547 0.41549 3.93939
94 2NVK NAP 0.003259 0.43346 3.97196
95 1O9U ADZ 0.002576 0.47279 4
96 4COQ SAN 0.01517 0.41451 4.04858
97 2W3L DRO 0.03695 0.41279 4.16667
98 3BRE C2E 0.006335 0.43205 4.18994
99 3KMT SAH 0.0006226 0.44153 4.20168
100 1I0Z OXM 0.01766 0.42954 4.2042
101 1I0Z NAI 0.00008387 0.41354 4.2042
102 4DYO SD4 0.003431 0.42722 4.20561
103 3CF6 SP1 0.002118 0.41688 4.20561
104 1UXG NAD 0.0003877 0.42309 4.20712
105 1UXG FUM 0.0003877 0.42309 4.20712
106 1YXM ADE 0.02025 0.41512 4.29043
107 1M5B BN1 0.004826 0.40342 4.56274
108 2FEQ 34P 0.003856 0.40333 4.6332
109 2FKA BEF 0.02855 0.40195 4.65116
110 1RZM E4P 0.007473 0.43483 4.73373
111 2Q1A 2KT 0.006681 0.43098 4.77816
112 2FR6 CTN 0.001294 0.41632 4.79452
113 2FR6 URI 0.001719 0.41199 4.79452
114 1ZJ6 G3D 0.004446 0.4132 4.81283
115 3DG6 MUC 0.001409 0.42799 4.90463
116 3FC4 EDO 0.003227 0.40698 4.90654
117 1WDA BAG 0.005912 0.41735 4.92537
118 3DGB MUC 0.008685 0.40175 4.97382
119 1XX4 BAM 0.01124 0.43972 4.98084
120 4B9E FAH 0.003057 0.45338 4.98339
121 4N9Z V3L 0.02596 0.42221 5.14019
122 2JBH 5GP 0.002667 0.43178 5.37383
123 3TO7 COA 0.001258 0.40699 5.43478
124 4IXW IXW 0.00447 0.42242 5.51181
125 3P7I P7I 0.004231 0.42858 5.60748
126 4K30 NLG 0.00548 0.42374 5.625
127 1MXI SAH 0.001381 0.41533 5.625
128 2YC5 6BC 0.000445 0.41745 5.70175
129 3LZW FAD 0.0005216 0.41904 5.72289
130 3LZW NAP 0.004348 0.40567 5.72289
131 4DN8 BMA 0.02638 0.40336 5.76923
132 1ZK7 FAD 0.0009821 0.41781 5.78158
133 3OND NAD 0.0007704 0.42317 5.84112
134 3OND ADN 0.0007704 0.42317 5.84112
135 1P9B HDA 0.02677 0.41076 5.84112
136 1FQK ALF 0.01756 0.42145 5.84615
137 3S9K CIT 0.006966 0.46205 5.9322
138 2FH5 GTP 0.002803 0.40087 5.94595
139 2Y7P SAL 0.01233 0.40853 5.9633
140 2JFV FLC 0.002848 0.44804 6.18557
141 2V6O FAD 0.005943 0.40941 6.20805
142 3A1I UNU 0.007753 0.40792 6.30841
143 1E4E PHY 0.003835 0.4073 6.41399
144 1ECM TSA 0.002246 0.43489 6.42202
145 2QCX PF1 0.001864 0.44997 6.46388
146 2ZWS PLM 0.0003548 0.54126 6.54206
147 4BWL MN9 0.0369 0.40423 6.57895
148 4PLG NAI 0.001308 0.40531 6.58683
149 4PLG OXM 0.001308 0.40531 6.58683
150 1Y75 NAG 0.00331 0.42787 6.77966
151 2WMO GTP 0.004938 0.4072 6.84211
152 1V7R CIT 0.0117 0.44663 7.00935
153 1VE3 SAM 0.003512 0.40106 7.04846
154 2BOI MFU 0.00803 0.41658 7.07965
155 2O66 FLC 0.009625 0.41822 7.40741
156 2C5S AMP 0.004575 0.422 7.47664
157 1SQ5 ADP 0.005925 0.40829 7.94393
158 1SQ5 PAU 0.01735 0.40211 7.94393
159 4DS0 A2G GAL NAG FUC 0.01456 0.42906 7.97546
160 1T0S BML 0.0008605 0.48806 8.13953
161 5A2J ALA PRO ASP THR ARG PRO 0.01412 0.43108 8.19672
162 1ZS6 ADP 0.003136 0.42885 8.28402
163 2ZJ5 ADP 0.002464 0.44458 8.41121
164 3E6J DR2 0.03412 0.41788 8.41121
165 3DDC GNP 0.0001893 0.41327 8.58896
166 1FIQ SAL 0.0007905 0.40573 8.85714
167 1QF5 RPL 0.002623 0.40576 8.8785
168 1QF5 GDP 0.002623 0.40576 8.8785
169 3BY8 MLT 0.003926 0.44819 9.15493
170 1BTN I3P 0.005733 0.47796 9.43396
171 2OFE NAG 0.004937 0.43704 9.85915
172 1QDS PGA 0.001863 0.433 9.96016
173 1G8S MET 0.01577 0.41374 10
174 3UEC ALA ARG TPO LYS 0.0373 0.40125 10.274
175 4JWX 1N4 0.002551 0.43804 11.0714
176 4F8L GAL 0.007065 0.4679 11.4486
177 1R37 NAD 0.0003963 0.41768 11.5274
178 3HCH RSM 0.03524 0.41383 11.6438
179 1ZX5 LFR 0.02074 0.40165 12.3333
180 2QGI UDP 0.03828 0.40255 12.3832
181 2E1A MSE 0.001606 0.44097 13.3333
182 2V5E SCR 0.01485 0.44102 14.5
183 3KJQ B94 0.001006 0.43856 16.8421
184 3CH5 GDP 0.006481 0.40675 17.3077
185 1YOA FMN 0.0472 0.42087 20.7547
186 1LNX URI 0.005525 0.42359 23.4568
187 1NU4 MLA 0.00307 0.48836 25.7732
188 2GCE SFC 0.00002041 0.42072 27.5
189 2GCE RFC 0.00004641 0.41324 27.5
190 2FYU FDN 0.003233 0.40233 28.5714
191 3QDT A2G GAL 0.003074 0.46066 32.1678
192 3QDY CBS 0.005032 0.44305 32.1678
193 3QDY A2G GAL 0.008095 0.43979 32.1678
194 1XA4 COA 0.0000005941 0.56716 39.486
195 1XVV CCQ 0.000002895 0.45768 41.6667
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