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Receptor
PDB id Resolution Class Description Source Keywords
4KCF 2.1 Å EC: 1.-.-.- X-RAY STRUCTURE OF A KIJD3 IN COMPLEX WITH FMN AND DTDP-3-AM TRIDEOXY-4-KETO-3-METHYL-D-GLUCOSE ACTINOMADURA KIJANIATA KIJD3 FATTY ACYL-COA DEHYDROGENASE FAMILY KIJANOSE KIJANIFAD FLAVOPROTEIN OXIDOREDUCTASE CLASS D FLAVIN CONTAININMONOOXYGENASES N-OXYGENASE NUCLEOTIDE LINKED SUGAR DTDP-236-TRIDEOXY-4-KETO-3-METHYL-D-GLUCOSE FMN
Ref.: ACTIVE SITE ARCHITECTURE OF A SUGAR N-OXYGENASE. BIOCHEMISTRY V. 52 3191 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AKM A:501;
Valid;
none;
submit data
561.371 C17 H29 N3 O14 P2 C[C@@...
FMN A:502;
Valid;
none;
submit data
456.344 C17 H21 N4 O9 P Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4KCF 2.1 Å EC: 1.-.-.- X-RAY STRUCTURE OF A KIJD3 IN COMPLEX WITH FMN AND DTDP-3-AM TRIDEOXY-4-KETO-3-METHYL-D-GLUCOSE ACTINOMADURA KIJANIATA KIJD3 FATTY ACYL-COA DEHYDROGENASE FAMILY KIJANOSE KIJANIFAD FLAVOPROTEIN OXIDOREDUCTASE CLASS D FLAVIN CONTAININMONOOXYGENASES N-OXYGENASE NUCLEOTIDE LINKED SUGAR DTDP-236-TRIDEOXY-4-KETO-3-METHYL-D-GLUCOSE FMN
Ref.: ACTIVE SITE ARCHITECTURE OF A SUGAR N-OXYGENASE. BIOCHEMISTRY V. 52 3191 2013
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 318 families.
1 4KCF - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3M9V - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 280 families.
1 4KCF - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3M9V - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 187 families.
1 4KCF - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3M9V - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AKM; Similar ligands found: 58
No: Ligand ECFP6 Tc MDL keys Tc
1 AKM 1 1
2 JHZ 0.74 0.974684
3 3YN 0.673267 0.924051
4 DWN 0.673267 0.949367
5 0N2 0.666667 0.962025
6 TTP 0.638298 0.886076
7 1JB 0.637255 0.924051
8 TRH 0.637255 0.924051
9 18T 0.637255 0.924051
10 TYD 0.630435 0.886076
11 T3F 0.625 0.949367
12 T3Q 0.625 0.949367
13 3R2 0.621359 0.936709
14 TDX 0.621359 0.911392
15 DAU 0.615385 0.9
16 0FX 0.613208 0.949367
17 T46 0.603774 0.924051
18 MMF 0.598131 0.925
19 TMP 0.593407 0.873418
20 QDM 0.587156 0.890244
21 TLO 0.582524 0.864198
22 FNF 0.581818 0.936709
23 1YF 0.581818 0.936709
24 4TG 0.576577 0.936709
25 QUH 0.542373 0.949367
26 FUH 0.542373 0.949367
27 T5A 0.5 0.83908
28 7SG 0.492537 0.860465
29 TQP 0.492537 0.860465
30 TBD 0.490196 0.853659
31 DT DT DT 0.481818 0.8625
32 T5K 0.467153 0.872093
33 T4K 0.467153 0.872093
34 DT DT DT DT DT 0.46087 0.8875
35 ATY 0.457944 0.911392
36 THM 0.456522 0.775
37 LLT 0.456522 0.775
38 UFP 0.454545 0.807229
39 DT DT PST 0.452991 0.821429
40 5HU 0.45 0.8625
41 0DN 0.446809 0.740741
42 NYM 0.445545 0.898734
43 THP 0.441176 0.860759
44 AZD 0.436364 0.833333
45 TPE 0.435897 0.888889
46 BRU 0.435644 0.807229
47 FDM 0.431373 0.819277
48 5IU 0.431373 0.807229
49 T3P 0.424242 0.8375
50 4TA 0.421053 0.806818
51 ATM 0.420561 0.821429
52 D3T 0.420561 0.8625
53 DUT 0.420561 0.848101
54 DT ME6 DT 0.418605 0.821429
55 TXS 0.411765 0.72619
56 DUD 0.409524 0.848101
57 BVP 0.407407 0.839506
58 T3S 0.403846 0.746988
Ligand no: 2; Ligand: FMN; Similar ligands found: 15
No: Ligand ECFP6 Tc MDL keys Tc
1 FMN 1 1
2 RBF 0.75641 0.876712
3 RS3 0.571429 0.831169
4 FAD 0.543307 0.876543
5 FAS 0.543307 0.876543
6 FAE 0.539062 0.865854
7 LFN 0.475 0.643836
8 C3F 0.473684 0.74359
9 CF4 0.463918 0.734177
10 FAY 0.446043 0.864198
11 FNR 0.444444 0.909091
12 RFL 0.442857 0.845238
13 4LS 0.411215 0.875
14 1VY 0.406593 0.769231
15 DLZ 0.404494 0.782051
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4KCF; Ligand: AKM; Similar sites found with APoc: 177
This union binding pocket(no: 1) in the query (biounit: 4kcf.bio4) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 1ZEI CRS None
3 4LHD GLY 1.10132
4 3TDC 0EU 1.32159
5 2UW1 GVM 1.47929
6 2RH1 CLR 1.54185
7 1GNI OLA 1.76211
8 4ARE FLC 1.98238
9 1U6R IOM 2.10526
10 4O6M C5P 2.15054
11 1EWF PC1 2.20264
12 3O01 DXC 2.27273
13 1VRP IOM 2.3622
14 3CV2 OXL 2.42291
15 5EE7 5MV 2.43363
16 3EQO LGC 2.5066
17 3X01 AMP 2.54453
18 5YSI NCA 2.63158
19 4QEK GLC 2.65781
20 1XX4 BAM 2.68199
21 1I0B PEL 2.71084
22 5UC4 83S 2.72727
23 3B1M KRC 2.82686
24 2P4Y C03 2.88809
25 5B0I BOG 2.91545
26 4NB5 2JT 2.92398
27 3FUR Z12 2.94118
28 3G9E RO7 2.95203
29 2VWA PTY 2.9703
30 5XJ7 87O 2.98507
31 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 3.06122
32 6CI9 F3V 3.0888
33 1E4I NFG 3.13199
34 3E85 BSU 3.16456
35 4G8R 96P 3.19149
36 2GBB CIT 3.20513
37 5EO8 TFU 3.21543
38 3KDU NKS 3.2491
39 4F4P 0SB 3.2967
40 3B9Z CO2 3.35052
41 5FYR INS 3.3557
42 1SBR VIB 3.5
43 1P7T PYR 3.52423
44 1UBY DMA 3.54223
45 2E2R 2OH 3.68852
46 1LNX URI 3.7037
47 4J26 EST 3.75
48 4J24 EST 3.75
49 1YC4 43P 3.78788
50 3PE2 E1B 3.85757
51 2BCG GER 3.8835
52 6BR9 PGV 3.89972
53 2WH8 II2 4.11622
54 1XVB 3BR 4.11765
55 4DE3 DN8 4.18251
56 5ECP JAA 4.18502
57 5ECP MET 4.18502
58 5ECP ATP 4.18502
59 5V3Y 5V8 4.1958
60 3B6C SDN 4.2735
61 4UCC ZKW 4.29185
62 2I74 MAN MAN MAN MAN 4.40529
63 5OLK DTP 4.40529
64 4L9Z OXL 4.42478
65 1HBK MYR 4.49438
66 1U3R 338 4.56432
67 5XSJ XYP 4.57516
68 5DX3 EST 4.5977
69 5DXG EST 4.5977
70 5WGD EST 4.5977
71 5DXE EST 4.5977
72 5WGQ EST 4.5977
73 5NTP 98E 4.62185
74 5HYR EST 4.65116
75 2QZO KN1 4.65116
76 3HYW DCQ 4.65116
77 2QA8 GEN 4.65116
78 4MG9 27K 4.70588
79 4MGB XDH 4.70588
80 4LWU 20U 4.70588
81 4MGA 27L 4.70588
82 3WYJ H78 4.74308
83 1M13 HYF 4.74684
84 5AAV GW5 4.7619
85 3UU7 2OH 4.78088
86 4TV1 36M 4.78088
87 3UUD EST 4.78088
88 2QE4 JJ3 4.83871
89 5IUY BOG 4.85651
90 4ZGM 32M 4.91803
91 5V4R MGT 4.93827
92 6CS8 F9Y 4.9505
93 4RW3 DKA 4.96689
94 4RW3 SHV 4.96689
95 3I6B KDO 5
96 4MNS 2AX 5.03145
97 5E70 RCD 5.06608
98 5CHR 4NC 5.10949
99 4L80 OXL 5.17241
100 3B6R CRN 5.24934
101 3KP6 SAL 5.29801
102 5KAU RHQ 5.45455
103 4MIB 28M 5.50661
104 6BR8 6OU 5.55556
105 6BR8 PGV 5.55556
106 1A0T SUC 5.56901
107 1OH2 SUC 5.56901
108 1A05 IPM 5.58659
109 6BJO DUY 5.6
110 4NAT ADP 5.625
111 5LX9 OLB 5.6338
112 4ZBR NPS 5.72687
113 4ZBR DIF 5.72687
114 4WGF HX2 5.85366
115 1DKF OLA 6.00858
116 4V2O CLQ 6.09756
117 5UNJ RJW 6.12245
118 4OAS 2SW 6.25
119 1TV5 N8E 6.32054
120 5AZC PGT 6.33333
121 3F8C HT1 6.34921
122 3SFI 3SF 6.35593
123 2BHW NEX 6.46552
124 6A5Y 9CR 6.57895
125 4OIV XX9 6.63717
126 5IM3 DTP 6.82819
127 1J78 OLA 6.82819
128 5HCV 60R 7.393
129 1I7M PUT 7.46269
130 5LWY OLB 7.47664
131 3DZ6 PUT 7.49064
132 1MID LAP 7.69231
133 4V3I ASP LEU THR ARG PRO 7.7821
134 5C9J DAO 8.08081
135 5U98 1KX 8.08081
136 5NNT DPV 8.10811
137 5WQJ 7N3 8.41751
138 2IDO TMP 8.43373
139 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 8.78661
140 3WFD AXO 8.90411
141 3RV5 DXC 8.98876
142 2WOR 2AN 9
143 3EW2 BTN 9.62963
144 1NF8 BOG 9.66184
145 6CS9 PIO 9.7561
146 6CB2 OLC 9.89761
147 4YSX E23 10.2837
148 4V1F BQ1 10.4651
149 1DTL BEP 10.559
150 3A06 FOM 10.9043
151 5OCA 9QZ 11.1111
152 6GD6 EVB 11.1111
153 3RMK BML 12.0482
154 1R6N 434 12.3223
155 1DQE BOM 12.4088
156 3E70 GDP 12.5
157 5W7B MYR 12.766
158 5M36 9SZ 13.1579
159 6GMN F4E 13.4021
160 1NU4 MLA 13.4021
161 2QQC AG2 15.0943
162 2QQD AG2 15.0943
163 1N13 AG2 15.3846
164 1MT1 AG2 15.3846
165 5W97 CHD 16.4384
166 5Z84 CHD 16.4384
167 5ZCO CHD 16.4384
168 2GJ5 VD3 17.284
169 5N8V KZZ 17.3913
170 3KPE TM3 17.9487
171 1M2Z BOG 19.0476
172 4F4S EFO 22.3684
173 2Y69 CHD 23.8095
174 5M37 9SZ 25
175 4OGQ 7PH 43.2432
176 4OGQ UMQ 43.2432
177 4OGQ SQD 43.2432
Pocket No.: 2; Query (leader) PDB : 4KCF; Ligand: AKM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4kcf.bio4) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4KCF; Ligand: FMN; Similar sites found with APoc: 54
This union binding pocket(no: 3) in the query (biounit: 4kcf.bio4) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 2F2G HMH 1.80995
2 2Q4X HMH 1.80995
3 6HKE LMR 1.88679
4 6HKE MLT 1.88679
5 3PA8 621 1.9685
6 5Y9D FAD 1.98238
7 1GPM AMP 2.20264
8 1U8V FAD 2.20264
9 3BMN AX3 2.43056
10 5HGZ MLA 2.88066
11 2GCG DGY 3.0303
12 2HK9 SKM 3.27273
13 4P86 5GP 3.82514
14 5MZN ADP 4.40529
15 5L1O 7PF 4.48878
16 3KP6 SAL 5.29801
17 2DDH FAD 5.72687
18 2DDH HXD 5.72687
19 5TCI MLI 6.88406
20 3KO0 TFP 6.93069
21 4Y9J UCC 7.48899
22 4Y9J FAD 7.48899
23 2YYJ FAD 9.03084
24 2YYJ 4HP 9.03084
25 1VG0 GER 9.17874
26 4NZF ARB 9.2511
27 5YS9 FAD 9.47137
28 4P83 U5P 10.989
29 3D9F FAD 12.1145
30 3D9F N6C 12.1145
31 3JQM GTP 12.7389
32 5ZW7 FAD 13.9303
33 3MKH FAD 17.8082
34 3DJL FAD 19.6035
35 5MR6 FAD 21.0654
36 2R0N TGC 21.3656
37 2R0N FAD 21.3656
38 6ES9 FAD 31.2775
39 4XVX P33 FDA 31.9383
40 4XVX P6G FDA 31.9383
41 3X0Y FMN 35.012
42 3B96 FAD 36.1233
43 1UDY CS8 36.3636
44 1UDY FAD 36.3636
45 1EGD FAD 36.6162
46 5AHS COA 36.6584
47 5AHS FAD 36.6584
48 3PFD FDA 37.659
49 3MPI GRA 38.2872
50 3MPI FAD 38.2872
51 1RX0 FAD 39.1857
52 1UKW FAD 39.314
53 1JQI FAD 40.9794
54 1BUC FAD 41.5144
Pocket No.: 4; Query (leader) PDB : 4KCF; Ligand: FMN; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4kcf.bio4) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 4KCF; Ligand: AKM; Similar sites found with APoc: 3
This union binding pocket(no: 5) in the query (biounit: 4kcf.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 4C01 QY9 2.83688
2 5LV1 78T 3.92857
3 5FH7 5XL 5.64516
Pocket No.: 6; Query (leader) PDB : 4KCF; Ligand: FMN; Similar sites found with APoc: 22
This union binding pocket(no: 6) in the query (biounit: 4kcf.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 3NYQ AMP 1.54185
2 3NYQ MCA 1.54185
3 1J6W MET 1.71429
4 5GUD 2IT 1.98238
5 5GUD NDP 1.98238
6 2H29 DND 2.6455
7 4ZAD 4LU 3.0837
8 4B2Z P5S 3.125
9 4G6I RS3 3.33333
10 4TWP AXI 4.05904
11 5A1T OXM 4.10557
12 3SMA ACO 4.54545
13 1PZG A3D 4.83384
14 3DOO SKM 5.41516
15 2Q46 NAP 5.5336
16 1YUC EPH 5.88235
17 1AJ0 PH2 6.73759
18 1AJ0 SAN 6.73759
19 5YU3 PRO 9.30233
20 5YU3 NAD 9.30233
21 1KGI T4A 10.2362
22 2C0U FAD NBT 12.1145
Pocket No.: 7; Query (leader) PDB : 4KCF; Ligand: AKM; Similar sites found with APoc: 4
This union binding pocket(no: 7) in the query (biounit: 4kcf.bio3) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 1MXG ACR 3.44828
2 2JHP GUN 4.34783
3 5URY PAM 5.47945
4 1VJE MSE 6.0241
Pocket No.: 8; Query (leader) PDB : 4KCF; Ligand: AKM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 4kcf.bio3) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 4KCF; Ligand: FMN; Similar sites found with APoc: 1
This union binding pocket(no: 9) in the query (biounit: 4kcf.bio3) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4ZAC 4LU 3.74449
Pocket No.: 10; Query (leader) PDB : 4KCF; Ligand: FMN; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 4kcf.bio3) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 4KCF; Ligand: AKM; Similar sites found with APoc: 2
This union binding pocket(no: 11) in the query (biounit: 4kcf.bio2) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 3JYY PPV 3.13589
2 2YJD YJD 3.75
Pocket No.: 12; Query (leader) PDB : 4KCF; Ligand: AKM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 4kcf.bio2) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 13; Query (leader) PDB : 4KCF; Ligand: AKM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 13) in the query (biounit: 4kcf.bio2) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 14; Query (leader) PDB : 4KCF; Ligand: AKM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 14) in the query (biounit: 4kcf.bio2) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 15; Query (leader) PDB : 4KCF; Ligand: FMN; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 15) in the query (biounit: 4kcf.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 16; Query (leader) PDB : 4KCF; Ligand: FMN; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 16) in the query (biounit: 4kcf.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 17; Query (leader) PDB : 4KCF; Ligand: FMN; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 17) in the query (biounit: 4kcf.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 18; Query (leader) PDB : 4KCF; Ligand: FMN; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 18) in the query (biounit: 4kcf.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
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