Structure of PDB 4dcx Chain A Binding Site BS01

Receptor Information
>4dcx Chain A (length=497) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAK
SWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLE
LANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHET
MNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDP
TTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLA
LNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYAN
LGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDAL
SKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPY
DPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYR
DILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKP
Ligand information
Ligand IDL2D
InChIInChI=1S/C22H28N4O4.Fe/c27-21(28)15-25(13-17-7-3-5-11-23-17)19-9-1-2-10-20(19)26(16-22(29)30)14-18-8-4-6-12-24-18;/h3-8,11-12,19-20H,1-2,9-10,13-16H2,(H,27,28)(H,29,30);/q;+2/p-2/t19-,20-;/m1./s1
InChIKeyRHFVCFXUQWXGET-GZJHNZOKSA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C1CC[C@@H]2[C@@H](C1)[N]34CC5=[N]([Fe]367([N]2(CC8=CC=CC=[N]68)CC(=O)O7)OC(=O)C4)C=CC=C5
OpenEye OEToolkits 1.7.6C1CCC2C(C1)[N]34CC5=[N]([Fe]367([N]2(CC8=CC=CC=[N]68)CC(=O)O7)OC(=O)C4)C=CC=C5
CACTVS 3.370O=C1CN|23Cc4ccccn4|[Fe]|5|6|2(O1)OC(=O)CN|5(Cc7ccccn|67)[C@@H]8CCCC[C@@H]38
ACDLabs 12.01O=C6O[Fe]2587OC(=O)CN8(Cc1n2cccc1)C3CCCCC3N7(Cc4ccccn45)C6
CACTVS 3.370O=C1CN|23Cc4ccccn4|[Fe]|5|6|2(O1)OC(=O)CN|5(Cc7ccccn|67)[CH]8CCCC[CH]38
FormulaC22 H26 Fe N4 O4
Name{2,2'-[(1R,2R)-cyclohexane-1,2-diylbis{[(pyridin-2-yl-kappaN)methyl]imino-kappaN}]diacetato-kappaO(2-)}iron;
Fe(1R,2R)-N,N'-Bis(2-pyridylmethyl)-N,N'-dicarboxymethyl-1,2-cyclohexanediamine
ChEMBL
DrugBank
ZINC
PDB chain4dcx Chain A Residue 630 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4dcx The structure of the periplasmic nickel-binding protein NikA provides insights for artificial metalloenzyme design.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		Y22 M27 W100 R137 W398 Y402 H416
Binding residue
(residue number reindexed from 1)		Y20 M25 W98 R135 W396 Y400 H414
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.50,Kd=31.4uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0016151 nickel cation binding
GO:0020037 heme binding
GO:0046914 transition metal ion binding
GO:0051540 metal cluster binding
GO:1904680 peptide transmembrane transporter activity
Biological Process
GO:0015675 nickel cation transport
GO:0015833 peptide transport
GO:0050919 negative chemotaxis
GO:0055085 transmembrane transport
GO:0098716 nickel cation import across plasma membrane
Cellular Component
GO:0016020 membrane
GO:0030288 outer membrane-bounded periplasmic space
GO:0042597 periplasmic space
GO:0043190 ATP-binding cassette (ABC) transporter complex
GO:0055052 ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4dcx, PDBe:4dcx, PDBj:4dcx
PDBsum4dcx
PubMed22526565
UniProtP33590|NIKA_ECOLI Nickel-binding periplasmic protein (Gene Name=nikA)

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