Receptor
PDB id Resolution Class Description Source Keywords
3E5P 2.5 Å EC: 5.1.1.1 CRYSTAL STRUCTURE OF ALANINE RACEMASE FROM E.FAECALIS ENTEROCOCCUS FAECALIS ALR ALANINE RACEMASE PLP SCP ISOMERASE PYRIDOXAL PHOSPH
Ref.: STRUCTURAL INSIGHTS INTO THE ALANINE RACEMASE FROM ENTEROCOCCUS FAECALIS. BIOCHIM.BIOPHYS.ACTA V.1794 1030 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
2PE C:401;
Invalid;
none;
submit data
414.488 C18 H38 O10 C(COC...
EPE A:430;
Invalid;
none;
submit data
238.305 C8 H18 N2 O4 S C1CN(...
PLP A:390;
B:390;
C:390;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
247.142 C8 H10 N O6 P Cc1c(...
PPI A:400;
B:400;
C:400;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
74.079 C3 H6 O2 CCC(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3E5P 2.5 Å EC: 5.1.1.1 CRYSTAL STRUCTURE OF ALANINE RACEMASE FROM E.FAECALIS ENTEROCOCCUS FAECALIS ALR ALANINE RACEMASE PLP SCP ISOMERASE PYRIDOXAL PHOSPH
Ref.: STRUCTURAL INSIGHTS INTO THE ALANINE RACEMASE FROM ENTEROCOCCUS FAECALIS. BIOCHIM.BIOPHYS.ACTA V.1794 1030 2009
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 3E5P - PPI C3 H6 O2 CCC(=O)O
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 3E5P - PPI C3 H6 O2 CCC(=O)O
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1BD0 - IN5 C10 H18 N2 O8 P2 Cc1c(c(c(c....
2 1XQK - PMH C11 H14 N3 O7 P Cc1c(c(c(c....
3 1XQL - PLP C8 H10 N O6 P Cc1c(c(c(c....
4 1FTX - EPC C10 H16 N2 O8 P2 Cc1c(c(c(c....
5 2SFP Ki = 20 mM PPI C3 H6 O2 CCC(=O)O
6 1L6G - PDD C11 H17 N2 O7 P Cc1c(c(c(c....
7 1NIU Ki = 0.08 uM DCS C11 H16 N3 O7 P Cc1c(c(c(c....
8 1L6F - PP3 C11 H17 N2 O7 P Cc1c(c(c(c....
9 2VD9 - EPC C10 H16 N2 O8 P2 Cc1c(c(c(c....
10 3E5P - PPI C3 H6 O2 CCC(=O)O
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PPI; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 PPI 1 1
2 BUA 0.5625 0.785714
3 2KT 0.5625 0.625
4 SMB 0.5 0.642857
5 LEA 0.473684 0.647059
6 AAE 0.470588 0.625
7 R3W 0.466667 0.642857
8 FAH 0.466667 0.642857
9 BXA 0.466667 0.642857
10 ACY 0.461538 0.636364
11 IVA 0.444444 0.714286
12 39J 0.4 0.6
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3E5P; Ligand: PPI; Similar sites found: 246
This union binding pocket(no: 1) in the query (biounit: 3e5p.bio2) has 5 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1HDR NAD 0.008037 0.48618 1.22951
2 3IB8 AMP 0.004029 0.48357 1.51515
3 3FPZ AHZ 0.02839 0.47394 1.53374
4 1TDF FAD 0.01383 0.46811 1.58228
5 1TDF NAP 0.04577 0.4579 1.58228
6 2AMV BIN 0.005122 0.49618 1.61725
7 3M6W SAM 0.01823 0.42606 1.61725
8 4KSY 1SY 0.004469 0.4619 1.65289
9 3IOI 1GW 0.02308 0.43939 1.67785
10 4DL8 UMP AF3 PO4 0.01046 0.45053 1.72414
11 3F3E LEU 0.03191 0.44836 1.7341
12 1R6W 164 0.03004 0.43667 1.86335
13 3P0K FAD 0.003935 0.48504 1.8797
14 3WD1 ST7 0.00129 0.54718 1.88679
15 1H82 FAD 0.005155 0.51153 1.88679
16 1H82 GZZ 0.01433 0.48212 1.88679
17 1ZGA HMK 0.005327 0.4577 1.96078
18 2H6T IVA VAL VAL STA ALA STA 0.0294 0.44006 2.05882
19 1P72 THM 0.01806 0.41249 2.09581
20 1FP1 HCC 0.002472 0.49417 2.15633
21 3MPI FAD 0.04669 0.4588 2.15633
22 3LPF Z77 0.009147 0.45784 2.15633
23 3MPI GRA 0.04853 0.44822 2.15633
24 2R42 FPS 0.02206 0.43413 2.15633
25 3BS8 PMP 0.03585 0.40518 2.15633
26 2J7T 274 0.01872 0.45147 2.31788
27 1VPM COA 0.02032 0.4397 2.36686
28 3I7S PYR 0.01657 0.40624 2.39726
29 2CKM AA7 0.003473 0.51145 2.42588
30 1KO0 LYS 0.002851 0.44714 2.42588
31 4RNX FMN 0.04264 0.43197 2.42588
32 1KO0 DLY 0.01975 0.42388 2.42588
33 3O7B SAH 0.0353 0.43567 2.45902
34 3S2Y FMN 0.003092 0.49176 2.51256
35 1SS4 CIT 0.001117 0.43114 2.61438
36 3VTF UPG 0.0002529 0.56417 2.69542
37 1B9I PXG 0.005544 0.48604 2.69542
38 2V6O FAD 0.04401 0.46054 2.69542
39 2ZYF AKG 0.01962 0.44013 2.69542
40 4NM5 ADP 0.02602 0.42449 2.69542
41 4AQL TXC 0.02727 0.42251 2.69542
42 1P9B IMO 0.03634 0.41913 2.69542
43 2WR8 SAH 0.01049 0.47268 2.7027
44 4USQ FAD 0.00328 0.5075 2.77008
45 1X8X TYR 0.04521 0.40198 2.79503
46 3DX5 DHB 0.0285 0.42611 2.7972
47 3S7O LBV 0.02526 0.43629 2.91545
48 3FS8 ACO 0.02029 0.48912 2.9304
49 4KXV TDP DX5 0.003811 0.49902 2.96496
50 3Q9T FAY 0.007428 0.48055 2.96496
51 4N4J HG1 0.01547 0.46132 2.96496
52 2IXB A2G 0.02531 0.45262 2.96496
53 2IXB NAD 0.0195 0.45262 2.96496
54 2P41 G1G 0.01505 0.42252 2.96496
55 4QDC ASD 0.04612 0.40961 2.96496
56 1UBY DMA 0.0254 0.41127 2.99728
57 1LL2 UPG 0.04475 0.4192 3.003
58 2UZ2 BTN 0.01711 0.43861 3.07692
59 2NT8 ATP 0.02306 0.45192 3.13901
60 1XX6 ADP 0.03584 0.40543 3.14136
61 1UJ2 ADP 0.003117 0.49901 3.1746
62 3P47 CYS 0.01812 0.42725 3.1746
63 2OKK ABU 0.001047 0.48002 3.2345
64 1DJ9 KAM 0.01017 0.46048 3.2345
65 1LC8 33P 0.01562 0.4416 3.2967
66 4IS0 1R4 0.005149 0.47097 3.3195
67 4IS0 GDS 0.04973 0.4103 3.3195
68 1GEX PLP HSA 0.03665 0.41238 3.37079
69 4N7C AEF 0.0008951 0.48334 3.40909
70 4FR3 0V4 0.03623 0.4554 3.4188
71 4FR3 LYS ARG ARG LYS SEP VAL 0.03623 0.4554 3.4188
72 3C1O NAP 0.04305 0.43872 3.42679
73 2JEN GLC GLC BGC XYS BGC XYS 0.03665 0.44803 3.44828
74 3IO3 ADP 0.01826 0.42104 3.44828
75 2XBN PMP 0.02919 0.43953 3.50404
76 4KCF AKM 0.02071 0.42994 3.50404
77 2YIV NBN 0.009404 0.42107 3.50404
78 3TO7 COA 0.03419 0.43637 3.62319
79 1B8U OAA 0.03754 0.4272 3.64742
80 4DQ2 BTX 0.01693 0.44582 3.65854
81 1F7K UMP 0.01374 0.45817 3.67647
82 2FFC U5P 0.01007 0.4569 3.68272
83 1SB8 UD2 0.03035 0.4511 3.69318
84 1NN5 ANP 0.01868 0.44586 3.72093
85 1NN5 2DT 0.01868 0.44586 3.72093
86 1Z6K OAA 0.01405 0.43657 3.75427
87 4Q3R XA2 0.01986 0.45348 3.77358
88 1NF8 BOG 0.02176 0.41413 3.86473
89 4LSJ LSJ 0.03351 0.44089 3.87597
90 2F01 BTN 0.004016 0.51703 3.93701
91 4C0X FMN 0.002004 0.51495 3.94089
92 4C0X AQN 0.002469 0.51495 3.94089
93 3ZS7 ATP 0.04955 0.41787 4
94 3UER BTU 0.0009825 0.50223 4.04313
95 3UER TUR 0.0009825 0.50223 4.04313
96 1ITZ TPP 0.008007 0.45177 4.04313
97 4LWA Q13 0.03531 0.4477 4.13223
98 4E1N TQX 0.0002775 0.56689 4.21687
99 3LZW NAP 0.03837 0.45448 4.21687
100 2F5T MAL 0.005416 0.4655 4.29185
101 4LN7 1ZQ 0.03712 0.43137 4.30622
102 2NS1 ADP 0.01066 0.46267 4.31034
103 3BL6 FMC 0.04204 0.42247 4.34783
104 4EKV BTN 0.004085 0.51203 4.40252
105 3VPQ GSH 0.01675 0.43601 4.41176
106 4MZ7 DGT 0.001014 0.53305 4.58221
107 4MZ7 DTP 0.001338 0.52332 4.58221
108 1BUC FAD 0.00389 0.50646 4.58221
109 1CL2 PPG 0.001727 0.49501 4.58221
110 4C0C WVH 0.04333 0.44807 4.58221
111 1QPB PYM 0.03397 0.42173 4.58221
112 1QPB TPP 0.03397 0.42173 4.58221
113 1NOW IFG 0.02844 0.41698 4.58221
114 1Q3P GLU ALA GLN THR ARG LEU 0.01997 0.42981 4.58716
115 3LM9 FRU 0.02541 0.43728 4.63576
116 3ZOD HQE 0.01633 0.44633 4.71204
117 3ZOD FMN 0.01633 0.44633 4.71204
118 3BLI ACO 0.03792 0.43961 4.74777
119 2C1Q BTN 0.001519 0.54831 4.7619
120 1ZCH FMN 0.01086 0.45752 4.85175
121 4KGM ATP 0.001495 0.50994 4.89796
122 4W6Z ETF 0.01926 0.41989 4.89914
123 2ZB3 NDP 0.04083 0.44419 5.09915
124 1M7Y PPG 0.0009017 0.54586 5.12129
125 2I4O ATP 0.004242 0.47449 5.12129
126 1YBH CIE 0.007737 0.44392 5.12129
127 3PXP MYR 0.02694 0.43963 5.13699
128 2NLI LAC 0.01146 0.50356 5.16304
129 1V9N NDP 0.001234 0.5423 5.27778
130 4K7O EKZ 0.009627 0.44371 5.35714
131 1S2D ADE 0.01435 0.44213 5.38922
132 3DDC GNP 0.005633 0.48848 5.42169
133 5CSM TRP 0.003744 0.47113 5.46875
134 1IYE PGU 0.02519 0.44921 5.50162
135 3ACC 5GP 0.04023 0.41234 5.52486
136 1Y52 BTN 0.0002892 0.57855 5.55556
137 1UKW FAD 0.0107 0.46235 5.66038
138 4NTX AMR 0.02592 0.40047 5.66038
139 3W54 RNB 0.02126 0.40941 5.77508
140 1MK1 APR 0.003975 0.49144 5.7971
141 2GJ3 FAD 0.01184 0.45743 5.83333
142 3WUC GLC GAL 0.0001464 0.53224 5.83942
143 1NOX FMN 0.001082 0.50837 5.85366
144 3WUD GLC GAL 0.0008471 0.48743 5.88235
145 3K3G MMU 0.0405 0.40922 5.88235
146 3B20 NAD 0.01478 0.44567 5.8997
147 1L1Q 9DA 0.04601 0.42802 5.91398
148 1VJO PLP 0.005995 0.45883 5.92992
149 2WQF FMN 0.008858 0.4563 5.94059
150 1POC GEL 0.04219 0.42662 5.97015
151 2HVW DCP 0.03445 0.42891 5.97826
152 1F8F NAD 0.01056 0.5018 6.19946
153 1MDZ PLP 0.03185 0.42999 6.19946
154 1MDZ DCS 0.03309 0.42999 6.19946
155 3SQG TP7 0.02101 0.42657 6.19946
156 4FDV 0UK 0.02052 0.44713 6.2201
157 2A0W DIH 0.02894 0.43469 6.22837
158 3TCT 3MI 0.03134 0.45105 6.29921
159 2PY4 DUP 0.01122 0.48051 6.32184
160 1MQ0 BRD 0.01544 0.44985 6.42857
161 2QJN KDG 0.01555 0.4427 6.46766
162 2P1O IHP 0.02768 0.44037 6.469
163 2P1O NLA 0.02768 0.44037 6.469
164 1WHT BZS 0.01482 0.43841 6.53595
165 1NW5 SAM 0.04518 0.4287 6.58307
166 1H9G COA MYR 0.02169 0.43329 6.58436
167 1YHM AHD 0.02989 0.40138 6.62983
168 4G09 0VD 0.03682 0.42913 6.73854
169 4INB 1F6 0.04173 0.43225 6.84932
170 4NAT 2W5 0.004035 0.49086 6.875
171 1KOL NAD 0.001392 0.54487 7.00809
172 1H16 COA 0.003209 0.48521 7.00809
173 1H16 PYR 0.01452 0.42949 7.00809
174 1RYI FAD 0.006579 0.49147 7.27763
175 1RYI GOA 0.01487 0.40205 7.27763
176 3H86 AP5 0.03872 0.45636 7.29167
177 2Q3M MLA 0.01794 0.41692 7.36196
178 1R6D NAD 0.01207 0.48548 7.4184
179 1R6D DAU 0.01288 0.4788 7.4184
180 1V1A ADP 0.00977 0.47507 7.44337
181 2W3L DRO 0.01015 0.43609 7.63889
182 3PVT 3HC 0.01209 0.48262 7.71704
183 1EP2 FAD 0.03942 0.44016 7.71704
184 2F7C CCU 0.03888 0.40884 7.72532
185 2P8O BVA 0.02803 0.41335 8.24742
186 1OLS TDP 0.003918 0.50481 8.35579
187 1Z42 FMN 0.01562 0.44038 8.57988
188 1Z42 HBA 0.007347 0.42475 8.57988
189 1Z44 NPO 0.0006636 0.41196 8.57988
190 4WX0 HXD 0.04726 0.42241 8.74525
191 1BGQ RDC 0.009803 0.45439 8.88889
192 4CO3 ATP 0.01269 0.47758 8.92857
193 2YDW WSH 0.02201 0.43932 9.15033
194 1QRD DQN 0.001686 0.46299 9.15751
195 1QRD FAD 0.01187 0.45172 9.15751
196 5XHA FRU FRU 0.001266 0.50779 9.16442
197 1ZK7 FAD 0.03345 0.45931 9.16442
198 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.002166 0.4591 9.18367
199 3TA2 ATP 0.02129 0.44724 9.32203
200 1HFS L04 0.01744 0.44012 9.375
201 3U5S FAD 0.005686 0.47241 9.52381
202 5FIT AP2 0.03403 0.40841 9.52381
203 4GO7 THR 0.003476 0.45696 10
204 2BS5 BGC GAL FUC 0.04313 0.43484 10
205 4NPT 017 0.006469 0.44024 10.101
206 1Y8O ADP 0.02701 0.43187 10.1562
207 4IHQ ADP 0.03257 0.42195 10.2426
208 3LEO GSH 0.005077 0.49735 10.3226
209 1A69 FMB 0.009977 0.48819 10.5042
210 3QDW A2G 0.0419 0.40185 11.1888
211 4BCS BTN 0.01021 0.43897 11.2
212 1I2B NAD 0.03042 0.47276 11.3208
213 1I2B UPG 0.03042 0.47276 11.3208
214 1I2B USQ 0.03042 0.47276 11.3208
215 1WUR 8DG 0.01442 0.44226 11.3636
216 1JYQ MAZ PTR PTM ASN 0.0009306 0.55346 11.4583
217 4HA6 FAD 0.01353 0.48279 11.5903
218 2XRH NIO 0.03137 0.40815 12
219 2ZSC BTN 0.001484 0.5022 12.0567
220 1NP0 NGT 0.02198 0.41817 12.069
221 1XHL TNE 0.01836 0.40808 12.4579
222 1UCN ADP 0.0197 0.44504 12.5
223 3SJ0 DXC 0.03559 0.40391 12.6761
224 1DUC DUD 0.003311 0.48884 12.6866
225 2VAR KDG 0.006543 0.46409 12.7796
226 2VAR KDF 0.01885 0.42954 12.7796
227 3O55 FAD 0.004015 0.49061 12.8
228 1R5A GTS 0.001283 0.50901 12.844
229 2YJ0 420 0.002223 0.53058 13.0435
230 2YJ0 FMN 0.001813 0.53058 13.0435
231 3CR4 PNT 0.008901 0.43685 13.0435
232 1JUV NDP 0.008724 0.46602 13.4715
233 3E81 SLB 0.03039 0.40791 14.0244
234 2ALG DAO 0.02913 0.4338 14.1304
235 2ALG HP6 0.02913 0.4338 14.1304
236 1HK8 DGT 0.008026 0.44318 15.0943
237 1Y7P RIP 0.03914 0.40565 15.6951
238 3PY5 AMP 0.03356 0.40236 16.0584
239 1XNK XS2 0.03599 0.42137 17.3469
240 3GB5 FMN 0.03571 0.42944 18.1467
241 1EZV UQ6 0.004377 0.47334 20
242 1EZV SMA 0.04554 0.44019 20
243 5E65 5N6 GAL 0.04296 0.42473 21.6867
244 1F7L COA 0.003564 0.51601 22.314
245 1B66 BIO 0.00336 0.49144 23.5714
246 3QP4 HL0 0.007788 0.45869 24.7253
Pocket No.: 2; Query (leader) PDB : 3E5P; Ligand: PPI; Similar sites found: 25
This union binding pocket(no: 2) in the query (biounit: 3e5p.bio1) has 7 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2GTE VA 0.01067 0.41692 1.6129
2 5V49 8WA 0.0141 0.44193 2.15633
3 3H4V NAP 0.01309 0.40239 2.43056
4 2RGO FAD 0.03109 0.40839 2.69542
5 4XRZ SI6 0.02803 0.42043 3.50404
6 3O5N BR0 0.00428 0.40929 3.57143
7 5X8I SQZ 0.001671 0.41931 3.75723
8 1RP0 AHZ 0.003985 0.41102 3.87324
9 4E13 NAD 0.01494 0.41775 3.88693
10 2EFJ SAH 0.00215 0.40249 4.04313
11 4DA6 GA2 0.007627 0.41219 4.34783
12 5F7J ADE 0.007512 0.41719 4.375
13 3W6X HZP 0.0009355 0.4013 4.80349
14 2PT9 S4M 0.0112 0.40881 4.98442
15 2PT9 2MH 0.0158 0.40881 4.98442
16 4YUW 4JU 0.03014 0.43228 5.26316
17 4YUW S4M 0.02977 0.43228 5.26316
18 3QXV MTX 0.001042 0.42014 5.55556
19 1NE7 16G 0.003576 0.40274 5.88235
20 1QX4 FAD 0.02459 0.42504 6.20438
21 2QRD ATP 0.008379 0.4107 8.24742
22 4FZV SAM 0.001273 0.45798 11.7155
23 3U3Z SEP GLN GLU PTR 0.02476 0.41122 14.0704
24 4QAR ADE 0.009071 0.41516 18.9055
25 1O94 AMP 0.01829 0.40099 20.2156
Pocket No.: 3; Query (leader) PDB : 3E5P; Ligand: PPI; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3e5p.bio1) has 6 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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