FAIRMol

Z56772918

Pose ID 12559 Compound 3661 Pose 358

DB SELECTIONDocking 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 Z56772918
PDB2WOV↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry high Native weak SASA done
Strain ΔE
22.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.19, Jaccard 0.13, H-bond role recall 0.00
Burial
91%
Hydrophobic fit
76%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.051 kcal/mol/HA) ✓ Good fit quality (FQ -9.93) ✓ Good H-bonds (4 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ High strain energy (22.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-29.439
kcal/mol
LE
-1.051
kcal/mol/HA
Fit Quality
-9.93
FQ (Leeson)
HAC
28
heavy atoms
MW
450
Da
LogP
5.67
cLogP
Strain ΔE
22.9 kcal/mol
SASA buried
91%
Lipo contact
76% BSA apolar/total
SASA unbound
663 Ų
Apolar buried
459 Ų

Interaction summary

HB 4 HY 24 PI 0 CLASH 2
Final rank1.790Score-29.439
Inter norm-1.145Intra norm0.039
Top1000noExcludedno
Contacts17H-bonds4
Artifact reasongeometry warning; 9 clashes; 1 protein clash; moderate strain Δ 22.9
Residues
ALA363 ALA365 ASP327 CYS52 CYS57 GLN439 GLY56 ILE438 LEU334 LYS60 NDP800 PHE367 PRO336 SER14 SER364 THR335 THR51

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

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 overlap5Native recall0.19
Jaccard0.13RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
404 0.8207185216231806 -0.836326 -19.773 5 16 0 0.00 0.00 - no Open
358 1.789900415573445 -1.14473 -29.4393 4 17 5 0.19 0.00 - no Current
384 1.8277656698694202 -0.884001 -22.3379 3 16 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 -29.439kcal/mol
Ligand efficiency (LE) -1.0514kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.926
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 450.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.67
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.92kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 75.14kcal/mol
Minimised FF energy 52.22kcal/mol

SASA & burial

✓ computed
SASA (unbound) 663.5Ų
Total solvent-accessible surface area of free ligand
BSA total 606.0Ų
Buried surface area upon binding
BSA apolar 458.9Ų
Hydrophobic contacts buried
BSA polar 147.2Ų
Polar contacts buried
Fraction buried 91.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3079.2Ų
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 1490.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)