Receptor
PDB id Resolution Class Description Source Keywords
4NMF 1.95 Å EC: 1.2.1.88_1.5.1.12 CRYSTAL STRUCTURE OF PROLINE UTILIZATION A (PUTA) FROM GEOBA SULFURREDUCENS PCA INACTIVATED BY N-PROPARGYLGLYCINE AND COW ITH MENADIONE BISULFITE GEOBACTER SULFURREDUCENS FLAVOENZYME ROSSMANN FOLD ALDEHYDE DEHYDROGENASE FLAVIN ADINUCLEOTIDE NICOTINAMIDE ADENINE DINUCLEOTIDE PROLINE CASUBSTRATE CHANNELING BIFUNCTIONAL ENZYME MECHANISM-BASED INACTIVATION OXIDOREDUCTASE
Ref.: STRUCTURES OF THE PUTA PERIPHERAL MEMBRANE FLAVOENZ REVEAL A DYNAMIC SUBSTRATE-CHANNELING TUNNEL AND TH QUINONE-BINDING SITE. PROC.NATL.ACAD.SCI.USA V. 111 3389 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:1103;
A:1104;
B:1106;
A:1105;
B:1105;
A:1106;
A:1107;
B:1104;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
P5F A:1101;
B:1101;
Invalid;
Invalid;
none;
none;
submit data
898.664 C32 H40 N10 O17 P2 CC1=C...
2L3 B:1102;
A:1102;
Valid;
Valid;
none;
none;
submit data
254.259 C11 H10 O5 S C[C@]...
2LB B:1103;
Valid;
none;
submit data
254.259 C11 H10 O5 S C[C@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4NMC 1.9 Å EC: 1.2.1.88_1.5.1.12 CRYSTAL STRUCTURE OF OXIDIZED PROLINE UTILIZATION A (PUTA) F GEOBACTER SULFURREDUCENS PCA COMPLEXED WITH ZWITTERGENT 3-1 GEOBACTER SULFURREDUCENS FLAVOENZYME ROSSMANN FOLD ALDEHYDE DEHYDROGENASE FLAVIN ADINUCLEOTIDE NICOTINAMIDE ADENINE DINUCLEOTIDE PROLINE CASUBSTRATE CHANNELING BIFUNCTIONAL ENZYME OXIDOREDUCTASE
Ref.: STRUCTURES OF THE PUTA PERIPHERAL MEMBRANE FLAVOENZ REVEAL A DYNAMIC SUBSTRATE-CHANNELING TUNNEL AND TH QUINONE-BINDING SITE. PROC.NATL.ACAD.SCI.USA V. 111 3389 2014
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4NMF - 2L3 C11 H10 O5 S C[C@]1(CC(....
2 4NM9 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 4NMA - TFB C5 H8 O3 C1C[C@H](O....
4 4NMB - 2OP C3 H6 O3 C[C@@H](C(....
5 4NMC - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
6 4NMD - FDA C27 H35 N9 O15 P2 Cc1cc2c(cc....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4NMF - 2L3 C11 H10 O5 S C[C@]1(CC(....
2 4NM9 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 4NMA - TFB C5 H8 O3 C1C[C@H](O....
4 4NMB - 2OP C3 H6 O3 C[C@@H](C(....
5 4NMC - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
6 4NMD - FDA C27 H35 N9 O15 P2 Cc1cc2c(cc....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4NMF - 2L3 C11 H10 O5 S C[C@]1(CC(....
2 4NM9 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 4NMA - TFB C5 H8 O3 C1C[C@H](O....
4 4NMB - 2OP C3 H6 O3 C[C@@H](C(....
5 4NMC - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
6 4NMD - FDA C27 H35 N9 O15 P2 Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 2L3; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 2LB 1 1
2 2L3 1 1
Ligand no: 2; Ligand: 2LB; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 2LB 1 1
2 2L3 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4NMC; Ligand: FAD; Similar sites found: 112
This union binding pocket(no: 1) in the query (biounit: 4nmc.bio1) has 38 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4KCT PYR 0.004371 0.45854 1.60321
2 4CQB MLI 0.04824 0.40494 1.65485
3 5JOX EDG 0.04721 0.40343 1.93798
4 4I9A NCN 0.01142 0.41728 2.08333
5 5BU2 AMP 0.02897 0.40009 2.20264
6 4IP7 FLC 0.007461 0.45107 2.20994
7 4M5P MLA 0.03712 0.42188 2.2113
8 5AHO TLA 0.04391 0.41655 2.38095
9 4AMW 5DI 0.02177 0.42639 2.38806
10 3EF0 ALF 0.02948 0.41755 2.41935
11 2G50 PYR 0.004378 0.46142 2.45283
12 5BRP PNG 0.009137 0.44451 2.46479
13 2BP1 FLC 0.01399 0.44542 2.5
14 4QDF 30Q 0.0262 0.40313 2.5641
15 3VC1 SAH 0.01395 0.40133 2.5641
16 1RZM E4P 0.02981 0.41934 2.66272
17 4A91 GLU 0.006701 0.45407 2.68456
18 5M12 7D0 0.01827 0.41773 2.78261
19 1JL0 PUT 0.0261 0.40787 2.99401
20 5KJW 53C 0.02608 0.42083 3.0445
21 5X7Q GLC GLC GLC GLC 0.006516 0.43493 3.18408
22 5X7Q GLC GLC GLC 0.008444 0.42737 3.18408
23 3APT FAD 0.0003287 0.45781 3.22581
24 5A07 GDP 0.01411 0.42736 3.22581
25 4RF7 ARG 0.03199 0.41143 3.48189
26 1P77 ATR 0.005573 0.45796 3.67647
27 2HKA C3S 0.02095 0.40174 3.84615
28 3UPY FOM 0.03495 0.40525 4.04494
29 3WV6 GAL BGC 0.0386 0.40769 4.39189
30 2EFE GNH 0.02136 0.40134 4.41989
31 5DG2 GAL GLC 0.02358 0.42743 4.44444
32 5H9O GLC 0.04282 0.4111 4.54545
33 5UN9 NHT 0.02665 0.40937 4.56349
34 3NZ1 3NY 0.0253 0.41581 4.5977
35 5L8N 6RQ 0.0328 0.40967 4.6875
36 3G5K BB2 0.02298 0.40592 4.91803
37 1AD4 HH2 0.01732 0.41531 5.26316
38 3ANY 2A3 0.04526 0.40251 5.32319
39 1WHT BZS 0.04711 0.40836 5.46875
40 5C1P ADP 0.02559 0.41027 5.55556
41 2YPI PGA 0.03308 0.40805 5.66802
42 1EYE PMM 0.01267 0.42581 5.71429
43 1LSS NAD 0.01728 0.40272 5.71429
44 2J5V RGP 0.04055 0.40992 5.72207
45 4KRI 1SH 0.02444 0.42296 5.77367
46 4UCC ZKW 0.03031 0.41259 6.00858
47 4M8E 29V 0.01381 0.40152 6.06061
48 2AJH MET 0.03169 0.4224 6.12245
49 1KTC NGA 0.03724 0.4129 6.17284
50 4LJ9 ACP 0.04522 0.40091 6.19469
51 5L95 AMP 0.00418 0.43084 6.25
52 3N9O OGA 0.02184 0.42377 6.25
53 4BQS ADP 0.0434 0.40185 6.25
54 4MG8 27J 0.02842 0.40459 6.27451
55 4TUZ 36J 0.03943 0.40065 6.27451
56 4XDA RIB 0.04581 0.40061 6.47249
57 4NZF ARB 0.0214 0.42611 6.47321
58 5DX3 EST 0.03913 0.40082 6.51341
59 5W3X IHP 0.02172 0.42155 6.53409
60 5W3Y ACO 0.02564 0.41796 6.53409
61 5W3Y IHP 0.02655 0.41688 6.53409
62 5BXV MGP 0.02792 0.41897 6.81818
63 1RHC F42 ACN 0.001561 0.42174 6.9697
64 4RW3 IPD 0.008696 0.44271 7.28477
65 5VLC HSO 0.04156 0.40643 7.3991
66 5K7U SAM 0.01972 0.40296 7.55556
67 5TCI 79V 0.01455 0.40052 7.56098
68 3OQJ 3CX 0.01514 0.42577 7.7821
69 5EXK MET 0.04866 0.40836 7.85498
70 2VEG PMM 0.03927 0.40775 7.96178
71 2YIP YIO 0.04696 0.41743 7.97101
72 5JDI 6JO 0.03919 0.41372 7.98611
73 5F74 AMP 0.03733 0.41284 8.13008
74 3EXS 5RP 0.02696 0.40911 8.1448
75 4YMU ARG 0.03703 0.41479 8.18182
76 3H8V ATP 0.005756 0.42788 8.21918
77 1W8S FBP 0.02409 0.40817 8.36502
78 4Q3F TLA 0.04546 0.40759 8.54701
79 2X1L ADN 0.03682 0.40926 8.58779
80 1S4P GDP 0.03298 0.40464 8.62069
81 4AFK FLC 0.01717 0.43479 8.73362
82 3VWX GSH 0.02456 0.42284 9.00901
83 4NAE 1GP 0.02676 0.42034 9.2511
84 2YMZ LAT 0.02539 0.42215 10
85 4BS0 6NT 0.02994 0.41409 10.6918
86 2XNJ NAP 0.01442 0.40632 10.9023
87 4RL4 PPV 0.004651 0.47261 11.3208
88 2FKA BEF 0.01937 0.40843 11.6279
89 2BOS GLA GAL GLC NBU 0.02919 0.41922 11.7647
90 3WG3 A2G GAL NAG FUC 0.04364 0.41008 12.3596
91 2WMC MGP 0.0464 0.40029 12.3596
92 4L8F MTX 0.03125 0.41707 12.5
93 3QH2 3NM 0.04095 0.41061 12.6697
94 5VE5 GSH 0.04436 0.40801 12.7321
95 3KDM TES 0.01514 0.43051 12.844
96 2HK9 ATR 0.03408 0.40737 13.0909
97 5H9Q TD2 0.03588 0.42208 13.5484
98 1UJP CIT 0.01152 0.41711 14.0221
99 1UO5 PIH 0.003086 0.44474 14.7059
100 1I7M PUT 0.02474 0.41052 14.9254
101 1B74 DGN 0.03576 0.42122 14.9606
102 4OSP 2V4 0.04969 0.40596 15.9696
103 4O8A FAD 3.449e-17 0.824 33.4789
104 3N9Q OGA 0.02578 0.41974 35.2941
105 1TIW FAD 9.542e-18 0.88558 40.1993
106 1TIW TFB 0.00000002248 0.40505 40.1993
107 3HAZ FAD 4.932e-16 0.89639 41.9901
108 5KF6 TFB 5.365e-18 0.94935 44.0796
109 5KF6 FAD 5.365e-18 0.94935 44.0796
110 4H6Q TFB 0.0000000000009291 0.78824 49.0385
111 4H6Q FAD 0.00000000001253 0.76895 49.0385
112 2G37 FAD 0.00000000003071 0.79007 49.8471
Pocket No.: 2; Query (leader) PDB : 4NMC; Ligand: 2OP; Similar sites found: 109
This union binding pocket(no: 2) in the query (biounit: 4nmc.bio1) has 37 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4KCT PYR 0.004166 0.45854 1.60321
2 5JOX EDG 0.0333 0.41064 1.93798
3 4I9A NCN 0.01086 0.41728 2.08333
4 5BU2 AMP 0.02796 0.40009 2.20264
5 4IP7 FLC 0.007131 0.45107 2.20994
6 4M5P MLA 0.0359 0.42188 2.2113
7 5AHO TLA 0.04239 0.41655 2.38095
8 4AMW 5DI 0.0209 0.42639 2.38806
9 3EF0 ALF 0.02839 0.41755 2.41935
10 2G50 PYR 0.004193 0.46142 2.45283
11 5BRP PNG 0.008769 0.44451 2.46479
12 2BP1 FLC 0.01346 0.44542 2.5
13 1RZM E4P 0.02871 0.41934 2.66272
14 4A91 GLU 0.006442 0.45407 2.68456
15 5M12 7D0 0.01746 0.41773 2.78261
16 1O68 KIV 0.04056 0.40989 2.90909
17 5KJW 53C 0.02508 0.42083 3.0445
18 5X7Q GLC GLC GLC GLC 0.006272 0.43493 3.18408
19 5X7Q GLC GLC GLC 0.008134 0.42737 3.18408
20 3APT FAD 0.0003874 0.45364 3.22581
21 5A07 GDP 0.01532 0.42449 3.22581
22 4RF7 ARG 0.03085 0.41143 3.48189
23 2CI5 HCS 0.047 0.40876 3.52113
24 3WJO IPE 0.04843 0.40608 3.56083
25 1P77 ATR 0.005322 0.45796 3.67647
26 2HKA C3S 0.01994 0.40174 3.84615
27 3UPY FOM 0.03371 0.40525 4.04494
28 3WV6 GAL BGC 0.0373 0.40769 4.39189
29 5DG2 GAL GLC 0.02277 0.42743 4.44444
30 5H9O GLC 0.0412 0.4111 4.54545
31 5UN9 NHT 0.02549 0.40937 4.56349
32 5L8N 6RQ 0.03156 0.40967 4.6875
33 4WUJ FMN 0.02169 0.40004 4.7619
34 3G5K BB2 0.02193 0.40592 4.91803
35 1M3U KPL 0.02831 0.41442 4.92424
36 3ANY 2A3 0.04365 0.40251 5.32319
37 5C1P ADP 0.02448 0.41027 5.55556
38 2YPI PGA 0.0317 0.40805 5.66802
39 1EYE PMM 0.01209 0.42581 5.71429
40 2J5V RGP 0.03905 0.40992 5.72207
41 4KRI 1SH 0.02344 0.42296 5.77367
42 4BHL ARG 0.02566 0.41735 5.89888
43 4UCC ZKW 0.0293 0.41259 6.00858
44 4M8E 29V 0.01309 0.40152 6.06061
45 2AJH MET 0.03636 0.41847 6.12245
46 1KTC NGA 0.03577 0.4129 6.17284
47 4LJ9 ACP 0.04339 0.40091 6.19469
48 3N9O OGA 0.02099 0.42377 6.25
49 5L95 AMP 0.009557 0.41343 6.25
50 4BQS ADP 0.04164 0.40185 6.25
51 4MG8 27J 0.02716 0.40459 6.27451
52 4XDA RIB 0.04396 0.40061 6.47249
53 4NZF ARB 0.02052 0.42611 6.47321
54 5DX3 EST 0.03749 0.40082 6.51341
55 5W3X IHP 0.02081 0.42155 6.53409
56 5W3X ACO 0.02547 0.42079 6.53409
57 5W3Y ACO 0.02465 0.41796 6.53409
58 5W3Y IHP 0.02545 0.41688 6.53409
59 1GVE CIT 0.04983 0.4048 6.72783
60 5BXV MGP 0.02691 0.41897 6.81818
61 1RHC F42 ACN 0.001529 0.42092 6.9697
62 1UAS GLA 0.04986 0.40121 7.18232
63 4RW3 IPD 0.008306 0.44271 7.28477
64 5K7U SAM 0.01877 0.40296 7.55556
65 5TCI 79V 0.01379 0.40052 7.56098
66 3OQJ 3CX 0.01447 0.42577 7.7821
67 5EXK MET 0.04685 0.40836 7.85498
68 2VEG PMM 0.0377 0.40775 7.96178
69 2YIP YIO 0.04535 0.41743 7.97101
70 5JDI 6JO 0.0377 0.41372 7.98611
71 3BMN NAP 0.003673 0.4062 7.98611
72 5F74 AMP 0.03586 0.41284 8.13008
73 3EXS 5RP 0.0258 0.40911 8.1448
74 4YMU ARG 0.03565 0.41479 8.18182
75 3H8V ATP 0.01815 0.40364 8.21918
76 1W8S FBP 0.02772 0.40415 8.36502
77 4Q3F TLA 0.02115 0.42641 8.54701
78 2X1L ADN 0.03534 0.40926 8.58779
79 1S4P GDP 0.03623 0.40158 8.62069
80 4NAE 1GP 0.02574 0.42034 9.2511
81 1H0A I3P 0.04524 0.40987 9.49367
82 2YMZ LAT 0.02453 0.42215 10
83 4BS0 6NT 0.02871 0.41409 10.6918
84 2XNJ NAP 0.01369 0.40632 10.9023
85 4RL4 PPV 0.01558 0.42907 11.3208
86 2FKA BEF 0.01868 0.40843 11.6279
87 2BOS GLA GAL GLC NBU 0.04297 0.40793 11.7647
88 3WG3 A2G GAL NAG FUC 0.04298 0.40953 12.3596
89 2WMC MGP 0.04485 0.40029 12.3596
90 4L8F MTX 0.03007 0.41707 12.5
91 3QH2 3NM 0.03468 0.41364 12.6697
92 5VE5 GSH 0.04278 0.40801 12.7321
93 3KDM TES 0.01988 0.42743 12.844
94 2HK9 ATR 0.03266 0.40737 13.0909
95 5H9Q TD2 0.03466 0.42208 13.5484
96 1UJP CIT 0.01095 0.41711 14.0221
97 1UO5 PIH 0.00297 0.44474 14.7059
98 1B74 DGN 0.03859 0.41904 14.9606
99 4OSP 2V4 0.04779 0.40596 15.9696
100 4O8A FAD 1.122e-16 0.82099 33.4789
101 3N9Q OGA 0.02479 0.41974 35.2941
102 1TIW FAD 1.881e-17 0.86673 40.1993
103 1TIW TFB 1.881e-17 0.86673 40.1993
104 3HAZ FAD 0.000000000000001665 0.87307 41.9901
105 5KF6 TFB 4.341e-18 0.94935 44.0796
106 5KF6 FAD 4.341e-18 0.94935 44.0796
107 4H6Q TFB 0.0000000000007985 0.78824 49.0385
108 4H6Q FAD 0.00000000001096 0.76895 49.0385
109 2G37 FAD 0.00000000002773 0.78968 49.8471
Pocket No.: 3; Query (leader) PDB : 4NMC; Ligand: FAD; 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: 4nmc.bio1) has 38 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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