FAIRMol

Z118508076

Pose ID 12668 Compound 3848 Pose 467

DB fairmolDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T19
T. brucei TR (NADPH binding site) T. brucei NADPH binding site
Ligand Z118508076
PDB2WOV↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native mixed SASA done
Strain ΔE
15.9 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.22, Jaccard 0.16, H-bond role recall 0.20
Burial
92%
Hydrophobic fit
71%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.194 kcal/mol/HA) ✓ Good fit quality (FQ -10.70) ✓ Good H-bonds (3 bonds) ✓ Deep burial (92% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ Moderate strain (15.9 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (3) ✗ Internal clashes (8)
Score
-28.666
kcal/mol
LE
-1.194
kcal/mol/HA
Fit Quality
-10.70
FQ (Leeson)
HAC
24
heavy atoms
MW
355
Da
LogP
3.70
cLogP
Strain ΔE
15.9 kcal/mol
SASA buried
92%
Lipo contact
71% BSA apolar/total
SASA unbound
570 Ų
Apolar buried
375 Ų

Interaction summary

HB 3 HY 20 PI 2 CLASH 2

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank0.195Score-28.666
Inter norm-1.299Intra norm0.105
Top1000noExcludedno
Contacts17H-bonds3
Artifact reasongeometry warning; 8 clashes; 3 protein contact clashes; 1 cofactor-context clash
Residues
ALA363 ALA365 CYS57 GLY56 ILE199 LEU334 LYS60 NDP800 PHE182 PHE203 PHE367 PRO336 SER178 SER364 THR335 THR51 VAL55

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name2WOVContacts27
PoseOpen native poseHB0
IFP residues
ALA284 ALA365 ARG222 ARG228 ARG287 ASN223 ASN254 GLN165 GLU202 GLY195 GLY196 GLY197 GLY286 ILE199 ILE285 LEU227 LEU334 LYS60 MET333 NDP800 PHE198 PHE367 PRO167 SER200 TYR221 VAL194 VAL366
Current overlap6Native recall0.22
Jaccard0.16RMSD-
HB strict1Strict recall0.08
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.25

Protein summary

493 residues
Protein targetT19Atoms7541
Residues493Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:330; TYR:294; ASP:264; MET:221

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
C:NDP800

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
467 0.19455200423800365 -1.29947 -28.6657 3 17 6 0.22 0.20 - no Current
470 1.5588883286034063 -1.12198 -36.4577 7 17 0 0.00 0.00 - no Open
487 1.9203568414870582 -1.37015 -40.0712 6 19 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -28.666kcal/mol
Ligand efficiency (LE) -1.1944kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.704
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 355.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.70
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 15.92kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -23.15kcal/mol
Minimised FF energy -39.07kcal/mol

SASA & burial

✓ computed
SASA (unbound) 569.6Ų
Total solvent-accessible surface area of free ligand
BSA total 525.8Ų
Buried surface area upon binding
BSA apolar 375.2Ų
Hydrophobic contacts buried
BSA polar 150.7Ų
Polar contacts buried
Fraction buried 92.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2984.4Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1482.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)