Receptor
PDB id Resolution Class Description Source Keywords
3BS8 2.3 Å EC: 5.4.3.8 CRYSTAL STRUCTURE OF GLUTAMATE 1-SEMIALDEHYDE AMINOTRANSFERA COMPLEXED WITH PYRIDOXAMINE-5'-PHOSPHATE FROM BACILLUS SUBT BACILLUS SUBTILIS GLUTAMATE-1-SEMIALDEHYDE 21-AMINOTRANSFERASE PORPHYRIN BIOSYNTHESIS ISOMERASE PYRIDOXAL PHOSPHATE
Ref.: CRYSTAL STRUCTURE OF GLUTAMATE1-SEMIALDEHYDE AMINOTRANSFERASE FROM BACILLUS SUBTILIS WITH BOUND PYRIDOXAMINE-5'-PHOSPHATE BIOCHEM.BIOPHYS.RES.COMMUN. V. 402 356 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PMP A:431;
 Valid;
 none;
 submit data
248.173 C8 H13 N2 O5 P Cc1c(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3BS8 2.3 Å EC: 5.4.3.8 CRYSTAL STRUCTURE OF GLUTAMATE 1-SEMIALDEHYDE AMINOTRANSFERA COMPLEXED WITH PYRIDOXAMINE-5'-PHOSPHATE FROM BACILLUS SUBT BACILLUS SUBTILIS GLUTAMATE-1-SEMIALDEHYDE 21-AMINOTRANSFERASE PORPHYRIN BIOSYNTHESIS ISOMERASE PYRIDOXAL PHOSPHATE
Ref.: CRYSTAL STRUCTURE OF GLUTAMATE1-SEMIALDEHYDE AMINOTRANSFERASE FROM BACILLUS SUBTILIS WITH BOUND PYRIDOXAMINE-5'-PHOSPHATE BIOCHEM.BIOPHYS.RES.COMMUN. V. 402 356 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3BS8 - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2HOZ - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
2 2GSA - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
3 3FQ8 - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
4 3FQ7 - PXG C15 H17 N2 O7 P Cc1c(c(c(c....
5 2HP1 - EA5 C13 H22 N3 O7 P Cc1c(c(c(c....
6 3FQA - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
7 3BS8 - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2HOZ - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
2 3FQ7 - PXG C15 H17 N2 O7 P Cc1c(c(c(c....
3 2HP1 - EA5 C13 H22 N3 O7 P Cc1c(c(c(c....
4 3BS8 - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PMP; Similar ligands found: 78
No: Ligand ECFP6 Tc MDL keys Tc
1 PMP 1 1
2 PXP 0.7 0.888889
3 GT1 0.673077 0.793103
4 PLG 0.57377 0.866667
5 IN5 0.57377 0.912281
6 P1T 0.571429 0.825397
7 PLR 0.557692 0.781818
8 2BO 0.553846 0.881356
9 TLP 0.553846 0.881356
10 2BK 0.553846 0.881356
11 PP3 0.546875 0.881356
12 PDA 0.546875 0.881356
13 PDD 0.546875 0.881356
14 ILP 0.544118 0.852459
15 33P 0.538462 0.896552
16 IK2 0.538462 0.825397
17 5PA 0.530303 0.825397
18 PLS 0.530303 0.866667
19 PMH 0.530303 0.742857
20 PLP 0.527273 0.767857
21 C6P 0.522388 0.866667
22 PPD 0.522388 0.866667
23 ORX 0.521127 0.854839
24 PXM 0.52 0.735849
25 PZP 0.517857 0.836364
26 PLA 0.514706 0.8125
27 PY5 0.514706 0.8125
28 PL2 0.514286 0.84127
29 QLP 0.514286 0.815385
30 PE1 0.513889 0.854839
31 PPG 0.513514 0.825397
32 P0P 0.508772 0.8
33 HEY 0.507042 0.8125
34 CBA 0.5 0.83871
35 PGU 0.5 0.83871
36 7TS 0.5 0.702703
37 EA5 0.5 0.828125
38 3LM 0.5 0.787879
39 PDG 0.5 0.83871
40 7XF 0.5 0.83871
41 9YM 0.493151 0.868852
42 LCS 0.492958 0.675676
43 PMG 0.492958 0.787879
44 DCS 0.492958 0.712329
45 76U 0.486111 0.825397
46 PY6 0.486111 0.787879
47 PL4 0.48 0.854839
48 PSZ 0.479452 0.8
49 N5F 0.479452 0.825397
50 4LM 0.462687 0.725806
51 0JO 0.462687 0.714286
52 AN7 0.461538 0.741379
53 PXG 0.460526 0.866667
54 RW2 0.460526 0.8
55 FOO 0.454545 0.75
56 PL8 0.454545 0.732394
57 GLY PLP 0.454545 0.779661
58 NPL 0.45 0.898305
59 KAM 0.448718 0.825397
60 1D0 0.444444 0.8
61 7B9 0.443038 0.764706
62 2B1 0.443038 0.690141
63 P3D 0.442857 0.85
64 PLP SER 0.441176 0.779661
65 EPC 0.439394 0.789474
66 MP5 0.438596 0.728814
67 EXT 0.432836 0.79661
68 PLP PMP 0.432836 0.770492
69 AQ3 0.426829 0.8125
70 2B6 0.426829 0.662162
71 PLP ALO 0.422535 0.833333
72 MPM 0.414286 0.75
73 KOU 0.408451 0.8
74 SER PLP 0.402778 0.813559
75 HCP 0.402778 0.741935
76 PLP 2TL 0.402778 0.79661
77 Z98 0.4 0.777778
78 PFM 0.4 0.770492
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3BS8; Ligand: PMP; Similar sites found: 220
This union binding pocket(no: 1) in the query (biounit: 3bs8.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1PTR PRB 0.003981 0.42719 None
2 2Z9V PXM 0.0008319 0.46622 1.02041
3 2FYF PLP 0.005722 0.41969 1.25628
4 1PEA ACM 0.001644 0.45231 1.2987
5 2ZWS PLM 0.03162 0.41277 1.36986
6 4N02 FNR 0.03312 0.40112 1.40056
7 4ME6 ADP 0.007324 0.40356 1.5544
8 2BLE 5GP 0.01476 0.42049 1.63488
9 2NCD ADP 0.005185 0.40982 1.66667
10 1GPJ CIT 0.00132 0.44132 1.73267
11 2IZ1 ATR 0.01562 0.40693 1.82648
12 2Q3M MLA 0.01232 0.41835 1.84049
13 1QO0 BMD 0.003398 0.4236 2.04082
14 2CE7 ADP 0.001572 0.40257 2.05479
15 3E5P PPI 0.03585 0.40518 2.15633
16 3TKA CTN 0.003576 0.46347 2.30548
17 3WCS MAN NAG 0.003517 0.41117 2.3622
18 3B8I OXL 0.0211 0.41411 2.43902
19 2OGA PGU 0.008909 0.41373 2.50627
20 3IHB GLU 0.008401 0.41262 2.51142
21 1Z45 GAL 0.005032 0.40492 2.51142
22 3IHB TRS 0.009546 0.40241 2.51142
23 3MAG 3MA 0.0232 0.41199 2.60586
24 1G8S MET 0.005681 0.41396 2.6087
25 3ZPG 5GP 0.002422 0.45285 2.6178
26 4N7U 2JA 0.00882 0.42546 2.63158
27 2VDJ HSE 0.01708 0.40476 2.65781
28 1GAD NAD 0.005542 0.40943 2.72727
29 1M32 PLP 0.006721 0.42218 2.73224
30 3I7S PYR 0.003596 0.43644 2.73973
31 3BRE C2E 0.01105 0.40145 2.7933
32 1E7S NAP 0.01236 0.40206 2.80374
33 2Q0D ATP 0.02646 0.40205 2.83286
34 1DJ9 KAM 0.0013 0.42377 2.86458
35 4HVK PMP 0.003132 0.41372 2.87958
36 1JGS SAL 0.002267 0.47439 2.89855
37 1YFZ IMP 0.005593 0.40845 2.92683
38 1ZUW DGL 0.004483 0.4018 2.94118
39 3UDG TMP 0.006639 0.43149 2.96804
40 3NKS ACJ 0.0005394 0.4106 2.96804
41 2BZ1 TAU 0.01204 0.43544 3.06122
42 1RYD GLC 0.002047 0.4331 3.10078
43 2XDQ MGX 0.001454 0.46364 3.19635
44 3FED BIX 0.004075 0.40074 3.19635
45 3U1T MLI 0.006325 0.41816 3.23625
46 1Y1A GSH 0.001025 0.49393 3.27869
47 2YD6 FLC 0.01255 0.44786 3.30189
48 1ULE GLA GAL NAG 0.002009 0.44825 3.33333
49 2EB5 OXL 0.006919 0.41026 3.37079
50 3ZRR PXG 0.0003441 0.42547 3.38542
51 2J0W ASP 0.0008996 0.45615 3.42466
52 1YBH P22 0.002788 0.40475 3.42466
53 3VPQ GSH 0.001304 0.43476 3.43137
54 2XUM OGA 0.00497 0.41647 3.4384
55 3RF4 FUN 0.003744 0.41008 3.44828
56 1TDF NAP 0.01232 0.43008 3.48101
57 4BAS GNP 0.005716 0.40091 3.51759
58 3LTW HLZ 0.002187 0.43187 3.57143
59 1WRA PC 0.01555 0.40058 3.57143
60 2YIV NBN 0.001524 0.4459 3.65297
61 2YIV YIV 0.005671 0.4272 3.65297
62 4WBD CIT 0.003043 0.43983 3.69686
63 2QLX RM4 0.01471 0.40167 3.7037
64 3P3N AKG 0.004557 0.4181 3.72493
65 1I0Z OXM 0.007709 0.42832 3.9039
66 1B74 DGN 0.007179 0.42241 3.93701
67 3L6R MLI 0.001275 0.44937 4.04624
68 1KC7 PPR 0.002828 0.43385 4.10959
69 2WGC SIA GAL BGC 0.01766 0.42647 4.10959
70 2PYU IMP 0.006129 0.40679 4.10959
71 1RQH PYR 0.01427 0.40225 4.10959
72 3UH0 TSB 0.00657 0.40196 4.10959
73 2YVF NAD 0.01987 0.4161 4.16667
74 2YVF FAD 0.01923 0.4161 4.16667
75 4OHB 5HM 0.001038 0.40181 4.21053
76 1XX4 BAM 0.006211 0.4329 4.21456
77 1JN2 SFP 0.01635 0.43156 4.21941
78 3BY8 MLT 0.006952 0.41632 4.22535
79 1HQL GLA MBG 0.004855 0.42332 4.28016
80 3BHO B4P 0.02032 0.41496 4.32692
81 3SQG COM 0.0007756 0.48743 4.3379
82 4HZO COA 0.001002 0.43308 4.40252
83 2O66 FLC 0.001137 0.43723 4.44444
84 3UWB BB2 0.00298 0.42606 4.54545
85 4C1K PEP 0.004098 0.4085 4.58015
86 1KO0 LYS 0.01263 0.41091 4.70588
87 1II5 GLU 0.002168 0.42558 4.72103
88 2F01 BTQ 0.04035 0.40422 4.72441
89 2F01 BTN 0.04035 0.40422 4.72441
90 2VQ5 HBA 0.005009 0.42272 4.97512
91 4B9E FAH 0.008142 0.41324 4.98339
92 1WDA BAG 0.004612 0.40132 5.02283
93 3S9K CIT 0.0001362 0.55418 5.08475
94 4LNL 2BK 0.00000314 0.48251 5.1051
95 4LNL PLG 0.0002632 0.46136 5.1051
96 4LNL 2BO 0.00025 0.45194 5.1051
97 2JFV FLC 0.004878 0.41682 5.15464
98 3CBG 4FE 0.0211 0.41411 5.17241
99 3CBG FER 0.01598 0.41282 5.17241
100 1GVF PGH 0.001877 0.42212 5.24476
101 4RJK PYR 0.001332 0.45657 5.25114
102 3P7I P7I 0.003375 0.41189 5.25114
103 3AHC TPP 0.009089 0.40498 5.25114
104 1WTC ACP 0.0075 0.41484 5.26316
105 1DFO PLG 0.003725 0.42993 5.27578
106 2PTZ PAH 0.001513 0.41455 5.32407
107 2CW6 3HG 0.01423 0.41528 5.36913
108 1U08 PLP 0.005104 0.41735 5.44041
109 1H16 PYR 0.01103 0.41368 5.47945
110 4GO7 THR 0.001265 0.41765 5.5
111 2Q8H TF4 0.003275 0.44646 5.65111
112 1BTN I3P 0.002399 0.47541 5.66038
113 4O8A 2OP 0.01425 0.41526 5.70776
114 2EFJ SAH 0.002811 0.40676 5.72917
115 1M1B SPV 0.006238 0.40647 5.76271
116 2BO4 FLC 0.004629 0.42425 5.79345
117 1Y7P RIP 0.0007984 0.45074 5.8296
118 3O03 GCO 0.00685 0.43082 5.84192
119 2X2T GAL NGA 0.000195 0.50612 5.88235
120 2XI7 XI7 0.01116 0.43722 5.97826
121 4W6Z ETF 0.0225 0.40552 6.05187
122 1U3I GSH 0.005111 0.41008 6.16114
123 1X54 4AD 0.006887 0.40274 6.2212
124 3L24 GOA 0.001366 0.46496 6.39269
125 1H8P PC 0.005436 0.43572 6.42202
126 1WHT BZS 0.007362 0.40909 6.53595
127 2DVZ GLU 0.003197 0.40252 6.6879
128 3B9Z CO2 0.007004 0.41003 6.70103
129 1FWV SGA MAG FUC 0.0158 0.41036 6.71642
130 1SC3 MLI 0.0001453 0.50147 6.81818
131 3GTD MLI 0.002627 0.42211 6.84932
132 1JHG TRP 0.005239 0.40963 6.93069
133 1C3V PDC 0.005688 0.40814 6.93878
134 3PD6 PMP 0.002558 0.43146 6.98254
135 3PDB PMP 0.003411 0.42094 6.98254
136 3QDY A2G GAL 0.002887 0.4409 6.99301
137 3QDV A2G 0.007087 0.4301 6.99301
138 3QDW A2G 0.008421 0.42644 6.99301
139 3QDT A2G GAL 0.01057 0.41453 6.99301
140 3QDV NDG 0.01065 0.40798 6.99301
141 3QDY CBS 0.01375 0.40299 6.99301
142 4K2M O1G 0.0003619 0.41056 7.07763
143 1C1L GAL BGC 0.004081 0.42671 7.29927
144 1O9U ADZ 0.01198 0.41894 7.71429
145 1H9G COA MYR 0.009278 0.40062 7.81893
146 1SS4 GSH 0.03301 0.41303 7.84314
147 2WCV FUC 0.002883 0.40925 7.85714
148 1AX2 NDG GAL 0.004916 0.40532 7.94979
149 3CQ5 PMP 0.0002779 0.44868 8.21918
150 1A5V Y3 0.004948 0.41066 8.22785
151 3K56 IS3 0.001412 0.40273 8.27068
152 2D37 FMN 0.004532 0.41287 8.52273
153 2D37 NAD 0.00493 0.41287 8.52273
154 1Z42 HBA 0.002841 0.4741 8.57988
155 1Z44 NPO 0.006881 0.44852 8.57988
156 3WJP ANP 0.002544 0.41046 8.57988
157 3PNL ADP 0.005822 0.40234 8.6758
158 2ALG DAO 0.0027 0.42162 8.69565
159 1O68 KIV 0.003638 0.41058 8.72727
160 1UW1 ADP 0.0006843 0.44641 8.75
161 4EXO PYR 0.007809 0.4207 8.90411
162 3VPD CIT 0.003367 0.45492 9.25267
163 3VPD BUA 0.029 0.41656 9.25267
164 3R51 MMA 0.0009869 0.47183 9.375
165 1LW4 TLP 0.00008689 0.50474 9.51009
166 1LW4 PLP 0.00006743 0.50474 9.51009
167 1Q3Q ANP 0.03083 0.40517 9.58904
168 4NPT 017 0.002316 0.40779 10.101
169 1GJW GLC 0.0005291 0.46648 10.274
170 1Q3P GLU ALA GLN THR ARG LEU 0.003348 0.40673 11.0092
171 1W3R PYR 0.01059 0.41449 11.1111
172 1VJO PLP 0.0007042 0.43555 11.1959
173 2ZE3 AKG 0.003041 0.41946 11.2727
174 1Y42 TYR 0.00144 0.42675 11.4796
175 2XRH NIO 0.003355 0.43053 12
176 4M5P MLA 0.0008381 0.48571 12.285
177 2Q97 ATP 0.000842 0.43458 12.4031
178 3F81 STT 0.005562 0.43524 12.5683
179 1YOA FMN 0.04854 0.40261 12.5786
180 1RYI GOA 0.02428 0.41466 13.089
181 3F8C HT1 0.003156 0.41879 13.4921
182 4AF5 CIT 0.0006523 0.45452 13.6842
183 4JCA CIT 0.01625 0.40118 14.3713
184 1NU4 MLA 0.01316 0.42464 15.4639
185 3W8S GSH 0.001669 0.43031 15.534
186 5DDW 5B6 0.003374 0.427 16.21
187 1T0S BML 0.002411 0.44455 16.2791
188 3UCJ AZM 0.004662 0.40114 16.2996
189 3WGC PLG 0.000158 0.46032 16.7155
190 1H2M OGA 0.0048 0.41712 17.3077
191 3I6B KDO 0.002013 0.4209 18.3333
192 3U7Y FLC 0.004889 0.46152 20.524
193 2XBN PMP 0.005836 0.429 21.5457
194 1NME 159 0.009088 0.42482 22.8261
195 1UO5 PIH 0.02156 0.42179 23.5294
196 1UO4 PIH 0.0222 0.41298 23.5294
197 4ZSY RW2 0.001408 0.4437 23.7443
198 2CJH AKG 0.000000008953 0.64136 24.0535
199 1I1Q TRP 0.003918 0.40408 25.5208
200 3UBW 6SP 0.0007925 0.50037 26.0536
201 2E1A MSE 0.0001089 0.46446 26.6667
202 4BA5 PXG 0.00000007609 0.59959 28.7671
203 1JAC AMG 0.01647 0.41964 30
204 3A8U PLP 0.00000000004717 0.69711 33.4076
205 2OAT PFM 0.002359 0.445 34.0183
206 2YLD CMO 0.006875 0.41038 34.6457
207 5G09 6DF 0.001004 0.45401 34.7032
208 1ZC9 PMP 0.00000000682 0.69769 35.1039
209 4UOX PLP 0.000000003273 0.6965 35.8447
210 4UOX PUT 0.00000002824 0.6154 35.8447
211 4UOX PLP PUT 0.00000006629 0.58537 35.8447
212 5WYF ILP 0.000357 0.47413 36.5297
213 4B98 PXG 0.00000003724 0.59412 37.2768
214 1MLY ACZ PLP 0.0000000933 0.64429 37.9953
215 4UHO PLP 0.000009917 0.60069 38.1279
216 4E3Q PMP 0.000000004317 0.70256 39.2694
217 1SFF IK2 0.000000007703 0.59091 39.4366
218 4ADC PLP 0.001828 0.43188 40.6404
219 2YKX AKG 0.001385 0.45172 47.2603
220 4AOA IK2 0.00000001314 0.62863 48.8584
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