FAIRMol

Z56854237

Pose ID 12652 Compound 5086 Pose 451

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 Z56854237
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 medium Native mixed SASA done
Strain ΔE
17.7 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.22, Jaccard 0.15, H-bond role recall 0.20
Burial
93%
Hydrophobic fit
92%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.256 kcal/mol/HA) ✓ Good fit quality (FQ -11.72) ✓ Deep burial (93% SASA buried) ✓ Lipophilic contacts well-matched (92%) ✗ Moderate strain (17.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-33.926
kcal/mol
LE
-1.256
kcal/mol/HA
Fit Quality
-11.72
FQ (Leeson)
HAC
27
heavy atoms
MW
436
Da
LogP
6.05
cLogP
Final rank
2.2142
rank score
Inter norm
-1.257
normalised
Contacts
18
H-bonds 4
Strain ΔE
17.7 kcal/mol
SASA buried
93%
Lipo contact
92% BSA apolar/total
SASA unbound
609 Ų
Apolar buried
524 Ų

Interaction summary

HBA 2 PC 1 HY 9 PI 1 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 1.

PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.

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

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
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
Jaccard0.15RMSD-
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
451 2.2142312747924273 -1.25712 -33.9265 4 18 6 0.22 0.20 - no Current

Molecular metrics

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

Scoring & efficiency
Docking score -33.926kcal/mol
Ligand efficiency (LE) -1.2565kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.723
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 435.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 6.05
Lipinski: ≤ 5
Rotatable bonds 2

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.75kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 133.22kcal/mol
Minimised FF energy 115.47kcal/mol

SASA & burial

✓ computed
SASA (unbound) 609.4Ų
Total solvent-accessible surface area of free ligand
BSA total 568.9Ų
Buried surface area upon binding
BSA apolar 524.2Ų
Hydrophobic contacts buried
BSA polar 44.7Ų
Polar contacts buried
Fraction buried 93.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 92.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3140.3Ų
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 1489.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)