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Receptor
PDB id Resolution Class Description Source Keywords
6C4A 1.8 Å EC: 4.1.3.1 CRYSTAL STRUCTURE OF 3-NITROPROPIONATE MODIFIED ISOCITRATE L MYCOBACTERIUM TUBERCULOSIS WITH PYRUVATE MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCTMC 107 / ERDMAN) LYASE
Ref.: THE NITRO GROUP AS A MASKED ELECTROPHILE IN COVALEN INHIBITION. ACS CHEM. BIOL. V. 13 1470 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3NP C:505;
B:502;
Invalid;
Invalid;
none;
none;
submit data
119.076 C3 H5 N O4 C(C[N...
MG F:505;
H:503;
B:501;
D:502;
G:504;
D:503;
H:504;
C:502;
G:506;
A:502;
H:501;
A:503;
F:503;
B:505;
E:502;
G:502;
B:504;
F:504;
C:503;
H:505;
E:503;
Part of Protein;
Part of Protein;
Invalid;
Part of Protein;
Part of Protein;
Part of Protein;
Invalid;
Part of Protein;
Invalid;
Part of Protein;
Invalid;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Invalid;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
PYR G:501;
B:503;
H:502;
D:501;
E:501;
C:501;
F:502;
A:501;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
88.062 C3 H4 O3 CC(=O...
EPE F:501;
G:503;
Invalid;
Invalid;
none;
none;
submit data
238.305 C8 H18 N2 O4 S C1CN(...
PEG G:505;
H:506;
C:504;
E:504;
F:506;
D:504;
B:506;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
106.12 C4 H10 O3 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6C4A 1.8 Å EC: 4.1.3.1 CRYSTAL STRUCTURE OF 3-NITROPROPIONATE MODIFIED ISOCITRATE L MYCOBACTERIUM TUBERCULOSIS WITH PYRUVATE MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCTMC 107 / ERDMAN) LYASE
Ref.: THE NITRO GROUP AS A MASKED ELECTROPHILE IN COVALEN INHIBITION. ACS CHEM. BIOL. V. 13 1470 2018
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 6C4A - PYR C3 H4 O3 CC(=O)C(=O....
2 1F8I - SIN C4 H6 O4 C(CC(=O)O)....
3 6C4C - PYR C3 H4 O3 CC(=O)C(=O....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6C4A - PYR C3 H4 O3 CC(=O)C(=O....
2 1F8I - SIN C4 H6 O4 C(CC(=O)O)....
3 6C4C - PYR C3 H4 O3 CC(=O)C(=O....
4 1IGW - PYR C3 H4 O3 CC(=O)C(=O....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6C4A - PYR C3 H4 O3 CC(=O)C(=O....
2 1F8I - SIN C4 H6 O4 C(CC(=O)O)....
3 6C4C - PYR C3 H4 O3 CC(=O)C(=O....
4 1IGW - PYR C3 H4 O3 CC(=O)C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PYR; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 PYR 1 1
2 ACY 0.636364 0.636364
3 OXD 0.545455 0.642857
4 F50 0.428571 0.6
5 2KT 0.411765 0.733333
6 AAE 0.411765 0.625
7 KIV 0.411765 0.785714
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6C4A; Ligand: PYR; Similar sites found with APoc: 94
This union binding pocket(no: 1) in the query (biounit: 6c4a.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 3UXL CFI 1.30548
2 2F2H XTG 1.35747
3 5IBE 69M 1.51515
4 2IHK CSF 1.58371
5 2IGA XX3 1.64384
6 4IPE ANP 1.80995
7 4A2B AGS 1.90931
8 4A2A ATP 1.90931
9 4JYD SAH 2.01149
10 5XWV 8H6 2.0362
11 4XPQ FUL 2.0362
12 1AL8 FMN 2.22841
13 4OUE IPT 2.26244
14 1TB3 FMN 2.27273
15 2AL2 PEP 2.29358
16 2AL2 2PG 2.29358
17 4IGH ORO 2.41935
18 4IGH 1EA 2.41935
19 4IGH FMN 2.41935
20 3JU6 ARG 2.43243
21 6BQC LOP 2.48869
22 2J62 GSZ 2.71493
23 2P53 NNG 2.71493
24 4XRZ SI6 2.71493
25 6DVH FMN 2.79188
26 5YSQ INS 2.7972
27 4N02 FNR 2.80112
28 4YUS FMN 2.87958
29 1M5W DXP 2.88066
30 1OFZ FUL 2.88462
31 1OFZ FUC 2.88462
32 2QZX IVA VAL VAL STA ALA STA 2.92398
33 2G50 PYR 2.94118
34 1DJX I3P 2.94118
35 5WBF LAC 2.96296
36 3EMY IVA VAL VAL STA ALA STA 3.03951
37 3B1Q NOS 3.06748
38 2Y7G AAE 3.19149
39 2C91 NAP 3.39367
40 2WQP WQP 3.4384
41 3GE7 AFQ 3.62694
42 1BXK NAD 3.66197
43 5MBC FMN 3.68272
44 1MEX RAC 3.72093
45 5T9C G3P 3.73134
46 5D2H AKG 3.88693
47 4TQK NAG 3.94089
48 1TV5 FMN 4.06321
49 1Q6O LG6 4.16667
50 4YFB PAC 4.29864
51 6EQS BV8 4.36364
52 2YAJ 4HP 4.65116
53 5XFV FMN 4.75113
54 2BJU IH4 4.75113
55 3WUG XYP 4.79233
56 3O9L LPN 4.81928
57 2TPS TPS 4.84582
58 1QIN GIP 4.91803
59 1FC4 AKB PLP 4.98753
60 6CI9 NAP 5.01931
61 3T7V MD0 5.14286
62 1LLO NAA NAA AMI 5.86081
63 3G6K FAD 6.16883
64 3G6K POP 6.16883
65 6BFG FMN 6.26566
66 2JBM SRT 6.35452
67 2IYG FMN 6.45161
68 1W8S FBP 6.46388
69 1YRX FMN 6.61157
70 3RFA SAM 6.68317
71 4K2G 1OQ 6.78733
72 1KKR 2AS 6.78733
73 5DEP UD1 6.97674
74 3VDB 149 7.46606
75 4UIB GWX 7.49186
76 2JG1 ANP 7.57576
77 1F8Y 5MD 7.64331
78 4EWN 0VR 7.90514
79 1M1B SPV 8.13559
80 1KBJ FMN 8.49515
81 1JQ3 AAT 9.12162
82 1O7Q UDP 9.34256
83 1O7Q GAL NAG 9.34256
84 4I54 1C1 10.7649
85 4D4U FUC GAL 13.0159
86 4D52 GXL 13.0159
87 3HQP OXL 14.2534
88 2ZE3 AKG 14.9091
89 3B8I OXL 14.9826
90 4DC2 ADE 25
91 2DUA OXL 25.1724
92 3M0J OAF 29.6417
93 1O5Q PYR 35.082
94 1XG4 ICT 37.2881
Pocket No.: 2; Query (leader) PDB : 6C4A; Ligand: PYR; Similar sites found with APoc: 22
This union binding pocket(no: 2) in the query (biounit: 6c4a.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 3WQT ANP 2.26244
2 4M26 SIN 2.47253
3 4M26 ZZU 2.47253
4 5LJW ANP 2.88184
5 1OX5 1PR 2.94118
6 2UYT ADP 2.94118
7 2UYT LRH 2.94118
8 1US2 XYP XYP XYP XYP 2.94118
9 2Z93 END 3.21101
10 2NX1 RP5 3.37079
11 2NX1 PEP 3.37079
12 2TPL HPP 3.61991
13 2Q3O FMN 4.09207
14 5HIP 61O 4.62046
15 3B1J NAD 4.71976
16 1JS3 PLP 142 5.34979
17 5GMD AGS 5.53846
18 6FE1 V14 6.22568
19 4AMF ACP 6.33484
20 2BP1 NDP 9.44444
21 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 10.5263
22 4K55 H6P 12.0968
Pocket No.: 3; Query (leader) PDB : 6C4A; Ligand: PYR; Similar sites found with APoc: 43
This union binding pocket(no: 3) in the query (biounit: 6c4a.bio2) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 5KXQ GDP 1.12994
2 4B0T ADP 1.58371
3 1KW6 BPY 1.71233
4 4L2H AR6 AR6 1.80995
5 4R74 F6P 1.86916
6 6ENO BJ8 1.90024
7 1P4C FMN 2.10526
8 5AEE NSQ 2.26244
9 1YOK P6L 2.34375
10 2FHK MFN 2.36486
11 2ZCQ B65 2.38908
12 2RDT 2RD 3.10078
13 2RDT FMN 3.10078
14 1EM6 NBG 3.16742
15 3VP6 HLD 3.39367
16 5LX9 OLA 3.52113
17 1GZ4 ATP 3.61991
18 5AYV KPL 3.61991
19 2EXK XYS XYS 3.84615
20 4KBS PX2 4.18605
21 2GJN FMN 4.26829
22 3UES DFU 4.29864
23 3RIY NAD 4.3956
24 4DK7 0KS 4.45344
25 2YIC TPP 4.52489
26 1S7G NAD 4.74308
27 2VHW NAI 4.77454
28 5DRB 5FJ 4.811
29 2AMT GPP 5.03145
30 3LL5 ADP 5.22088
31 3LL5 IPE 5.22088
32 2J4K U5P 5.30973
33 3LZW FAD 6.3253
34 2ZFZ ARG 6.32911
35 6HOY TSN 6.33484
36 1O68 KIV 6.54545
37 4TXE 38F 6.80272
38 5JIC N7E 7.32601
39 5JIC ADP 7.32601
40 3WRB GDE 8.37321
41 4JB1 NAP 8.82353
42 6CAY ERG 8.87574
43 4AVB ACO 14.7147
Pocket No.: 4; Query (leader) PDB : 6C4A; Ligand: PYR; Similar sites found with APoc: 9
This union binding pocket(no: 4) in the query (biounit: 6c4a.bio2) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 1VEM GLC GLC 2.48869
2 4IP7 FLC 2.94118
3 2OFW ADX 3.36538
4 5EPO TUD 3.81679
5 5IRR GSP 3.8961
6 2VEG PMM 4.4586
7 6HOY AR6 6.33484
8 2ET1 GLV 7.46269
9 4KCT PYR 9.27602
Pocket No.: 5; Query (leader) PDB : 6C4A; Ligand: PYR; Similar sites found with APoc: 44
This union binding pocket(no: 5) in the query (biounit: 6c4a.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 4D1J DGJ 1.58371
2 5OES 3GC 1.58371
3 4D42 NAP 2.12766
4 4D42 W0I 2.12766
5 3MJY IJZ 2.31214
6 3MJY FMN 2.31214
7 5YSS NAD 2.34375
8 5UY8 AMZ 2.48869
9 5NBW 8SK 2.7027
10 2JFN GLU 2.94118
11 6AR9 3L4 2.94118
12 3ZGJ RMN 2.96496
13 1M3U KPL 3.0303
14 5ZW7 FAD 3.16742
15 2D24 XYS XYS 3.21101
16 5THQ NDP 3.30882
17 5NXX 3Q7 3.35821
18 1XT8 CYS 3.42466
19 3V1S 0LH 3.72671
20 1EP2 ORO 3.85852
21 1W62 PYC 3.86473
22 4C01 QY9 3.90071
23 2YJP CYS 4.12371
24 4AZC NGW 4.29864
25 1OFD FMN 4.75113
26 3CEV ARG 5.01672
27 6CI9 F3V 5.01931
28 2GZM DGL 5.24345
29 4OIT BMA 5.30973
30 4OIT MAN 5.30973
31 3PCJ INO 5.88235
32 2VWT PYR 5.99251
33 1KJ1 MAN 6.42202
34 4EUO ABU 7.1875
35 1PVN MZP 7.44681
36 6CGZ HL6 7.80142
37 4LED XXR 7.83582
38 4UP4 GAL NAG 7.98005
39 2O1O RIS 8.15217
40 2P7Q GG6 8.27068
41 5CKS GAL 8.83191
42 5JSP DQY 8.95522
43 5LWY OLB 10.2804
44 4X6F 3XU 12.381
Pocket No.: 6; Query (leader) PDB : 6C4A; Ligand: PYR; Similar sites found with APoc: 15
This union binding pocket(no: 6) in the query (biounit: 6c4a.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 4O4Z N2O 1.2987
2 3MKK GLC BGC 2.0362
3 4XOE KGM 2.15054
4 5YBN AKG 2.54777
5 2VK2 GZL 2.61438
6 2HFK E4H 2.82132
7 5D6T NGA 2.94118
8 4BG4 ARG 2.94118
9 5YF9 NIO 4.12979
10 1FFU CDP 4.29864
11 4XDA RIB 4.85437
12 1R1Q ACE ARG GLU PTR VAL ASN VAL 5
13 5V7I GLY 6.93277
14 5ME4 HP4 8.0292
15 1M5B BN1 11.4068
Pocket No.: 7; Query (leader) PDB : 6C4A; Ligand: PYR; Similar sites found with APoc: 15
This union binding pocket(no: 7) in the query (biounit: 6c4a.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 4OKZ 3E9 1.36986
2 1QFT HSM 2.28571
3 4A38 BZS 2.31959
4 5E4R 40E 2.71493
5 5UKL SIX 2.94985
6 4WNK 453 3.16742
7 4GC1 MAN MAN 3.62319
8 4XDZ 40E 4.08163
9 2OG7 SIN 5.04202
10 2DWU DGL 5.43478
11 5CSD ACD 5.66038
12 5MB4 NAG 7.98005
13 2B4B B33 12.2807
14 5IDB BMA 14.7887
15 5IDB MAN 14.7887
Pocket No.: 8; Query (leader) PDB : 6C4A; Ligand: PYR; Similar sites found with APoc: 4
This union binding pocket(no: 8) in the query (biounit: 6c4a.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 5AB1 BCD TA5 HP6 MAN 2
2 1ZUW DGL 2.20588
3 2P9H IPT 2.97398
4 3GJB AKG 5.64263
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