Receptor
PDB id Resolution Class Description Source Keywords
2MBR 1.8 Å EC: 1.1.1.158 MURB WILD TYPE, COMPLEX WITH ENOLPYRUVYL-UDP-N- ACETYLGLUCOSAMINE ESCHERICHIA COLI PEPTIDOGLYCAN SYNTHESIS CELL WALL CELL DIVISION OXIDOREDUCTASE NADP FLAVOPROTEIN FAD
Ref.: X-RAY CRYSTAL STRUCTURES OF THE S229A MUTANT AND WILD-TYPE MURB IN THE PRESENCE OF THE SUBSTRATE ENOLPYRUVYL-UDP-N-ACETYLGLUCOSAMINE AT 1.8-A RESOLUTION. BIOCHEMISTRY V. 36 806 1997
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EPU A:402;
Valid;
none;
submit data
677.4 C20 H29 N3 O19 P2 CC(=O...
FAD A:401;
Valid;
none;
submit data
785.55 C27 H33 N9 O15 P2 Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2MBR 1.8 Å EC: 1.1.1.158 MURB WILD TYPE, COMPLEX WITH ENOLPYRUVYL-UDP-N- ACETYLGLUCOSAMINE ESCHERICHIA COLI PEPTIDOGLYCAN SYNTHESIS CELL WALL CELL DIVISION OXIDOREDUCTASE NADP FLAVOPROTEIN FAD
Ref.: X-RAY CRYSTAL STRUCTURES OF THE S229A MUTANT AND WILD-TYPE MURB IN THE PRESENCE OF THE SUBSTRATE ENOLPYRUVYL-UDP-N-ACETYLGLUCOSAMINE AT 1.8-A RESOLUTION. BIOCHEMISTRY V. 36 806 1997
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1MBB - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 1UXY - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 2MBR - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1MBB - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 1UXY - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 2MBR - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1MBB - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 1UXY - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 2MBR - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
4 4JB1 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
5 4JAY - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: EPU; Similar ligands found: 67
No: Ligand ECFP6 Tc MDL keys Tc
1 EPU 1 1
2 EPZ 0.770642 0.957747
3 EEB 0.747748 0.944444
4 UD2 0.742857 0.971429
5 UD1 0.742857 0.971429
6 U20 0.704918 0.85
7 U21 0.704918 0.85
8 UMA 0.697479 0.957747
9 HP7 0.681818 0.957143
10 MJZ 0.675676 0.930556
11 UD7 0.666667 0.943662
12 GUD 0.644231 0.957143
13 UFM 0.644231 0.957143
14 GDU 0.644231 0.957143
15 UPG 0.644231 0.957143
16 UD4 0.640351 0.930556
17 UDZ 0.632479 0.87013
18 UAG 0.626866 0.906667
19 U2F 0.611111 0.905405
20 UPF 0.611111 0.905405
21 UGA 0.6 0.942857
22 UGB 0.6 0.942857
23 U22 0.6 0.829268
24 UFG 0.59633 0.905405
25 UDM 0.587719 0.930556
26 12V 0.584746 0.917808
27 HWU 0.584746 0.917808
28 UML 0.575342 0.85
29 USQ 0.571429 0.814815
30 UAD 0.567568 0.929577
31 UDX 0.567568 0.929577
32 UDP 0.554455 0.901408
33 UTP 0.553398 0.901408
34 G3N 0.552632 0.90411
35 UD0 0.542253 0.8375
36 URM 0.540541 0.916667
37 660 0.540541 0.916667
38 4RA 0.528169 0.848101
39 UPU 0.527778 0.928571
40 IUG 0.524194 0.804878
41 UNP 0.523364 0.876712
42 3UC 0.521368 0.905405
43 U5P 0.49505 0.887324
44 UPP 0.491228 0.902778
45 UDH 0.491228 0.833333
46 UDP GAL 0.487179 0.929577
47 2KH 0.477064 0.876712
48 C5G 0.470588 0.905405
49 44P 0.466667 0.864865
50 2QR 0.458333 0.839506
51 Y6W 0.457627 0.88
52 UDP UDP 0.453704 0.873239
53 UP5 0.44697 0.822785
54 UAG API 0.440994 0.858974
55 2GW 0.440945 0.944444
56 4TC 0.42963 0.802469
57 1GW 0.428571 0.906667
58 CSV 0.425197 0.844156
59 CSQ 0.425197 0.844156
60 U 0.424242 0.828571
61 URI 0.424242 0.828571
62 PMP UD1 0.417219 0.8125
63 CJB 0.411765 0.814286
64 UMA FGA LYS DAL DAL 0.406977 0.8375
65 U U 0.406504 0.888889
66 U3P 0.401869 0.873239
67 UA3 0.401869 0.873239
Ligand no: 2; Ligand: FAD; Similar ligands found: 119
No: Ligand ECFP6 Tc MDL keys Tc
1 FAS 1 1
2 FAD 1 1
3 FAY 0.859259 0.9875
4 RFL 0.852941 0.963855
5 6FA 0.794118 0.987654
6 DAL FAD PER 0.772414 0.951807
7 FAE 0.751773 0.987654
8 SFD 0.651007 0.860215
9 FDA 0.641892 0.906977
10 FNK 0.602564 0.876405
11 62F 0.572327 0.939024
12 F2N 0.566265 0.886364
13 FMN 0.543307 0.876543
14 FA9 0.526316 0.939759
15 6YU 0.516304 0.860215
16 CNV FAD 0.511905 0.908046
17 P6G FDA 0.511628 0.908046
18 FAD NBT 0.508876 0.83871
19 A2D 0.504065 0.875
20 P5F 0.491329 0.941176
21 FAD CNX 0.488506 0.8125
22 APR 0.488372 0.851852
23 AR6 0.488372 0.851852
24 AGS 0.484615 0.811765
25 SAP 0.484615 0.811765
26 M33 0.484375 0.864198
27 BA3 0.484127 0.875
28 FAD NBA 0.480663 0.802083
29 ATP 0.48062 0.851852
30 B4P 0.480315 0.875
31 ADP 0.480315 0.851852
32 AP5 0.480315 0.875
33 ANP 0.477273 0.831325
34 AQP 0.476923 0.851852
35 5FA 0.476923 0.851852
36 48N 0.469388 0.902439
37 OAD 0.467626 0.876543
38 GTA 0.465753 0.892857
39 AN2 0.465116 0.841463
40 AD9 0.462121 0.831325
41 3OD 0.460993 0.876543
42 RBF 0.460938 0.790123
43 FB0 0.460606 0.835165
44 139 0.460526 0.858824
45 AP0 0.46 0.835294
46 A22 0.459854 0.864198
47 ACP 0.458015 0.853659
48 8QN 0.456522 0.864198
49 PRX 0.454545 0.831325
50 A1R 0.453237 0.86747
51 G3A 0.452055 0.902439
52 T5A 0.45098 0.872093
53 G5P 0.44898 0.902439
54 ATF 0.448529 0.821429
55 50T 0.44697 0.819277
56 ACQ 0.444444 0.853659
57 PAJ 0.442857 0.847059
58 ADQ 0.442857 0.853659
59 5AL 0.441176 0.864198
60 ADX 0.439394 0.775281
61 CA0 0.439394 0.853659
62 A4P 0.437909 0.831461
63 25L 0.4375 0.864198
64 P33 FDA 0.436464 0.817204
65 5SV 0.435714 0.793103
66 TXE 0.434211 0.890244
67 OMR 0.434211 0.818182
68 ABM 0.434109 0.829268
69 A 0.433071 0.82716
70 AMP 0.433071 0.82716
71 4AD 0.432624 0.855422
72 ADJ 0.432258 0.818182
73 BIS 0.430556 0.802326
74 SRA 0.429688 0.788235
75 AFH 0.42953 0.825581
76 TXD 0.427632 0.890244
77 NXX 0.427632 0.865854
78 UP5 0.427632 0.878049
79 DND 0.427632 0.865854
80 6V0 0.427632 0.857143
81 SRP 0.42446 0.843373
82 PR8 0.423611 0.837209
83 TAT 0.423358 0.821429
84 AMO 0.422535 0.865854
85 PTJ 0.42069 0.835294
86 FYA 0.42069 0.864198
87 TXA 0.42069 0.865854
88 CNA 0.420382 0.865854
89 00A 0.41958 0.823529
90 AHX 0.41958 0.835294
91 MAP 0.41844 0.811765
92 NAI 0.418301 0.845238
93 AU1 0.41791 0.831325
94 AP2 0.416667 0.843373
95 A12 0.416667 0.843373
96 25A 0.415493 0.851852
97 AMP MG 0.415385 0.785714
98 COD 0.415094 0.842697
99 ADP BEF 0.414815 0.77907
100 BEF ADP 0.414815 0.77907
101 4TC 0.412903 0.879518
102 APC 0.411765 0.843373
103 NB8 0.410959 0.835294
104 ME8 0.410959 0.806818
105 1ZZ 0.410959 0.806818
106 4UW 0.409091 0.825581
107 NAX 0.409091 0.837209
108 RBY 0.408759 0.843373
109 ADV 0.408759 0.843373
110 ADP MG 0.407407 0.797619
111 P1H 0.405882 0.818182
112 OOB 0.405594 0.864198
113 A A 0.40411 0.829268
114 LAD 0.40411 0.825581
115 UPA 0.403846 0.86747
116 4UU 0.401316 0.833333
117 A3D 0.401235 0.876543
118 DLL 0.4 0.864198
119 XAH 0.4 0.806818
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2MBR; Ligand: EPU; Similar sites found: 101
This union binding pocket(no: 1) in the query (biounit: 2mbr.bio1) has 54 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3F4F UMP 0.01059 0.43601 None
2 3LRE ADP 0.02478 0.43242 1.47059
3 5GJC ATP 0.03384 0.42023 1.47059
4 2OG2 MLI 0.0002953 0.5581 1.76471
5 2Q4W FAD 0.0001349 0.46797 1.76471
6 3NHB ADP 0.04645 0.42098 1.96078
7 4PPF FLC 0.002859 0.49428 2.05882
8 4KBF AMP 0.03929 0.4203 2.05882
9 1X14 NAD 0.03317 0.40788 2.05882
10 1OJ4 ANP 0.0389 0.4044 2.12014
11 2I0K FAD 0.0001468 0.46366 2.35294
12 5LTJ BEF 0.01957 0.44153 2.35294
13 5XDR ADP 0.01611 0.43386 2.35294
14 5TSH ADP 0.04313 0.42346 2.35294
15 5E5U MLI 0.005013 0.44126 2.51256
16 2PS1 ORO 0.006761 0.46262 2.65487
17 2PS1 PRP 0.03583 0.40078 2.65487
18 1GOJ ADP 0.02019 0.44382 2.94118
19 1OXV ANP 0.04945 0.4147 2.94118
20 3UIE ANP 0.03917 0.41676 3
21 2VOH CIT 0.03354 0.43517 3.18471
22 4P8K 38C 0.00001985 0.4572 3.23529
23 4P8K FAD 0.00001985 0.4572 3.23529
24 2WM4 VGJ 0.04599 0.40074 3.23529
25 3KC1 2T6 0.03827 0.40201 3.2641
26 2FJK 13P 0.0494 0.41123 3.27869
27 5J75 6GQ 0.0431 0.40798 3.40909
28 4AG5 ADP 0.003846 0.48405 3.52941
29 5XQL C2E 0.006439 0.49935 3.78007
30 2W58 ADP 0.0107 0.45654 3.9604
31 4QM7 GTP 0.0275 0.42514 4.09357
32 1E8G FCR 0.0001291 0.44971 4.11765
33 1E8G FAD 0.000151 0.4449 4.11765
34 3A4M ADP 0.01961 0.44138 4.11765
35 3ZGE ASP 0.04852 0.41729 4.11765
36 3W8X FAD 0.0001191 0.40851 4.11765
37 4IEE AGS 0.0135 0.44606 4.41176
38 1JI0 ATP 0.04578 0.42036 4.58333
39 3SRV S19 0.03727 0.41129 4.69314
40 2DPY ADP 0.02508 0.4353 4.70588
41 2D2F ADP 0.04748 0.41255 4.8
42 1JJV ATP 0.0355 0.42904 4.85437
43 4E03 ADP 0.03529 0.42291 4.85437
44 4YMU ATP 0.02603 0.43027 5
45 3B9Q MLI 0.001311 0.51948 5.29801
46 2DT9 THR 0.02942 0.42731 5.38922
47 1O5O U5P 0.04554 0.40985 5.42986
48 3UEC ALA ARG TPO LYS 0.04569 0.4207 5.47945
49 2XCF BBQ 0.03664 0.40571 5.55556
50 1YQT ADP 0.04223 0.42381 5.58824
51 4CVN ADP 0.0338 0.42791 5.83942
52 2GK6 ADP 0.03189 0.42935 5.88235
53 4JWX 1N4 0.04758 0.41939 6.07143
54 4YDS ATP 0.009214 0.45993 6.14035
55 2AWN ADP 0.006018 0.47646 6.17647
56 4YSW FAD 0.0004229 0.40349 6.17647
57 3WD6 GSH 0.04258 0.41834 6.25
58 1QKQ MAN 0.04267 0.41055 6.33803
59 4AUT FAD 0.00002321 0.48453 6.47059
60 1GMN IDS SGN IDS SGN IDS 0.04461 0.42291 6.55738
61 1FFU FAD 0.0003634 0.4461 6.74847
62 3BJU ATP 0.04638 0.40631 6.76471
63 5GVR LMR 0.001066 0.5304 6.83761
64 4PL8 ATP 0.02205 0.41093 7.05882
65 3V2U ATP 0.01987 0.41035 7.05882
66 4PKI ATP 0.02636 0.40721 7.05882
67 4PKG ATP 0.02717 0.40657 7.05882
68 1KXP ATP 0.03185 0.40325 7.05882
69 2FF6 ATP 0.03327 0.40234 7.05882
70 4P83 U5P 0.04611 0.41287 7.14286
71 2X1L MET 0.0498 0.42033 7.35294
72 3FIU POP 0.04512 0.42097 7.63052
73 5G5G FAD 0.0001149 0.45147 7.64706
74 2WHX ADP 0.03333 0.42929 7.64706
75 2UZH IPE 0.02547 0.43496 7.87879
76 2UUU FAD 0.00002118 0.44936 7.94118
77 2UUU PL3 0.00002118 0.44936 7.94118
78 1N62 FAD 0.0003498 0.44168 7.94118
79 1T3Q FAD 0.0002375 0.45037 8.23529
80 2WEL K88 0.04973 0.41877 8.25688
81 1RM6 FAD 0.00005882 0.4643 8.69565
82 4E28 9MZ 0.03725 0.42727 8.92308
83 2XT3 ADP 0.02144 0.44323 9.41177
84 5JWI ARG GLU 0.02472 0.41426 9.41177
85 1FW1 GSH 0.04565 0.40667 9.72222
86 1UGY GLA GLC 0.03152 0.43249 9.77444
87 3HRD FAD 0.0001017 0.40592 9.7973
88 4CBX ATP 0.03395 0.40191 10.2362
89 2CBZ ATP 0.02018 0.44181 12.2363
90 1F0X FAD 0.00006958 0.46719 12.6471
91 1JJ7 ADP 0.02108 0.43785 12.6923
92 3NRZ FAD 0.0004439 0.44542 13.4146
93 1GXU 2HP 0.0007815 0.50521 14.2857
94 4P5E N6P 0.02836 0.40306 14.4737
95 2O1C PPV 0.04805 0.4342 15.3333
96 3LN9 FLC 0.04726 0.41252 17.2662
97 1G6H ADP 0.02025 0.43885 18.677
98 2A40 ATP 0.02611 0.40741 21.875
99 4U00 ADP 0.01429 0.45034 28.2787
100 1JAC AMG 0.04958 0.40551 40
101 2A3Z ATP 0.0285 0.40558 41.3793
Pocket No.: 2; Query (leader) PDB : 2MBR; Ligand: FAD; Similar sites found: 105
This union binding pocket(no: 2) in the query (biounit: 2mbr.bio1) has 55 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3F4F UMP 0.006436 0.44767 None
2 3LRE ADP 0.02541 0.43242 1.47059
3 5GJC ATP 0.03324 0.42132 1.47059
4 2OG2 MLI 0.0003044 0.5581 1.76471
5 2Q4W FAD 0.00006201 0.48191 1.76471
6 3NHB ADP 0.04764 0.42098 1.96078
7 4PPF FLC 0.002942 0.49428 2.05882
8 4KBF AMP 0.04036 0.4203 2.05882
9 2WW4 ADP 0.04467 0.41095 2.12014
10 1OJ4 ANP 0.04008 0.4044 2.12014
11 2I0K FAD 0.00007015 0.47676 2.35294
12 5XDR ADP 0.0166 0.43386 2.35294
13 5TSH ADP 0.04424 0.42346 2.35294
14 5E5U MLI 0.005138 0.44126 2.51256
15 5AE2 FAD 0.00003291 0.40814 2.64706
16 5AE2 FYC 0.00003291 0.40814 2.64706
17 2PS1 ORO 0.006972 0.46262 2.65487
18 2PS1 PRP 0.03104 0.40446 2.65487
19 1GOJ ADP 0.02071 0.44382 2.94118
20 3UIE ANP 0.04026 0.41676 3
21 4O08 PO6 0.03622 0.42783 3.11526
22 2VOH CIT 0.03429 0.43517 3.18471
23 4P8K FAD 0.000009314 0.46862 3.23529
24 4P8K 38C 0.000009314 0.46862 3.23529
25 3KC1 2T6 0.03946 0.40201 3.2641
26 5J75 6GQ 0.04435 0.40798 3.40909
27 4AG5 ADP 0.003964 0.48405 3.52941
28 5K62 ASN VAL 0.04832 0.41965 3.52941
29 4PFT MAB 0.03682 0.41222 3.52941
30 2HQU DUP 0.01438 0.42052 3.65854
31 5XQL C2E 0.006598 0.49935 3.78007
32 2XAU ADP 0.02573 0.42035 3.82353
33 2W58 ADP 0.01099 0.45654 3.9604
34 4QM7 GTP 0.02813 0.42527 4.09357
35 1E8G FCR 0.0001334 0.45012 4.11765
36 1E8G FAD 0.0001561 0.44531 4.11765
37 3A4M ADP 0.02016 0.44138 4.11765
38 3ZGE ASP 0.04966 0.41729 4.11765
39 1V97 FAD 0.0002797 0.408 4.11765
40 3W8X FAD 0.0001212 0.40584 4.11765
41 2Y91 98J 0.03011 0.41197 4.15094
42 4IEE AGS 0.01391 0.44606 4.41176
43 1JI0 ATP 0.04698 0.42036 4.58333
44 3SRV S19 0.03836 0.41129 4.69314
45 2DPY ADP 0.02578 0.4353 4.70588
46 2D2F ADP 0.04859 0.41255 4.8
47 1JJV ATP 0.03643 0.42904 4.85437
48 4E03 ADP 0.03626 0.42291 4.85437
49 4YMU ATP 0.02677 0.43027 5
50 3B9Q MLI 0.001349 0.51948 5.29801
51 1O5O U5P 0.03439 0.41704 5.42986
52 3UEC ALA ARG TPO LYS 0.0468 0.4207 5.47945
53 2XCF BBQ 0.03776 0.40571 5.55556
54 1YQT ADP 0.04332 0.42381 5.58824
55 4CVN ADP 0.03471 0.42791 5.83942
56 2GK6 ADP 0.03275 0.42935 5.88235
57 4JWX 1N4 0.04882 0.41939 6.07143
58 4YDS ATP 0.009489 0.45993 6.14035
59 2AWN ADP 0.006184 0.47646 6.17647
60 4YSW FAD 0.0002513 0.41157 6.17647
61 4YSW NAI 0.0003146 0.40882 6.17647
62 3WD6 GSH 0.04365 0.41834 6.25
63 2H92 C5P 0.04598 0.41028 6.39269
64 4AUT FAD 0.000009262 0.50009 6.47059
65 1GMN IDS SGN IDS SGN IDS 0.04557 0.42289 6.55738
66 1FFU FAD 0.0002103 0.45589 6.74847
67 3BJU ATP 0.04771 0.40631 6.76471
68 5GVR LMR 0.001097 0.5304 6.83761
69 4PL8 ATP 0.02278 0.41093 7.05882
70 3V2U ATP 0.02055 0.41035 7.05882
71 4PKI ATP 0.02722 0.40721 7.05882
72 4PKG ATP 0.02806 0.40657 7.05882
73 1KXP ATP 0.03287 0.40325 7.05882
74 2FF6 ATP 0.03434 0.40234 7.05882
75 4P83 U5P 0.04532 0.41394 7.14286
76 3FIU POP 0.03806 0.42552 7.63052
77 5G5G FAD 0.00008475 0.45703 7.64706
78 2WHX ADP 0.03421 0.42929 7.64706
79 2UZH IPE 0.02616 0.43496 7.87879
80 2UUU FAD 0.000008018 0.46325 7.94118
81 2UUU PL3 0.000008018 0.46325 7.94118
82 1N62 FAD 0.000158 0.45514 7.94118
83 1T3Q FAD 0.00009934 0.46526 8.23529
84 4K33 ACP 0.03799 0.40283 8.30769
85 1RM6 FAD 0.00002908 0.47612 8.69565
86 4E28 9MZ 0.0382 0.42727 8.92308
87 2XT3 ADP 0.02202 0.44323 9.41177
88 5JWI ARG GLU 0.0255 0.41426 9.41177
89 1FW1 GSH 0.04696 0.40667 9.72222
90 1UGY GLA GLC 0.03226 0.43249 9.77444
91 3HRD FAD 0.00004694 0.41323 9.7973
92 4CBX ATP 0.03504 0.40191 10.2362
93 1B7A OPE 0.0333 0.42127 10.7527
94 3IP8 B85 0.04522 0.41399 12.0968
95 2CBZ ATP 0.0207 0.44181 12.2363
96 1F0X FAD 0.00005044 0.47324 12.6471
97 1JJ7 ADP 0.02163 0.43785 12.6923
98 3NRZ FAD 0.0002006 0.4594 13.4146
99 1GXU 2HP 0.0008043 0.50521 14.2857
100 2O1C PPV 0.0491 0.4342 15.3333
101 3LN9 FLC 0.04829 0.41252 17.2662
102 1G6H ADP 0.02078 0.43885 18.677
103 2A40 ATP 0.02696 0.40741 21.875
104 4U00 ADP 0.01467 0.45034 28.2787
105 2A3Z ATP 0.02942 0.40558 41.3793
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