FAIRMol

Z56821488

Pose ID 12731 Compound 2608 Pose 530

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 Z56821488
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 medium Native mixed SASA done
Strain ΔE
19.5 kcal/mol
Protein clashes
3
Internal clashes
5
Native overlap
contact recall 0.30, Jaccard 0.22, H-bond role recall 0.20
Burial
91%
Hydrophobic fit
79%
Reason: no major geometry red flags detected
3 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.052 kcal/mol/HA) ✓ Good fit quality (FQ -10.04) ✓ Good H-bonds (3 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Moderate strain (19.5 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Internal clashes (9)
Score
-30.513
kcal/mol
LE
-1.052
kcal/mol/HA
Fit Quality
-10.04
FQ (Leeson)
HAC
29
heavy atoms
MW
447
Da
LogP
5.33
cLogP
Final rank
0.5250
rank score
Inter norm
-1.134
normalised
Contacts
18
H-bonds 5
Strain ΔE
19.5 kcal/mol
SASA buried
91%
Lipo contact
79% BSA apolar/total
SASA unbound
676 Ų
Apolar buried
489 Ų

Interaction summary

HBD 1 HBA 2 HY 7 PI 0 CLASH 5

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.

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

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 overlap8Native recall0.30
Jaccard0.22RMSD-
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
530 0.5250301583940824 -1.13446 -30.5126 5 18 8 0.30 0.20 - no Current
558 1.4699525519425631 -0.921866 -19.6322 4 16 0 0.00 0.00 - no Open
536 1.9079564582586215 -0.936292 -22.7415 2 16 0 0.00 0.00 - no Open
563 2.0566042597876093 -0.771845 -14.9745 2 18 0 0.00 0.00 - no Open
532 2.1972836050937206 -0.843441 -14.8348 1 17 0 0.00 0.00 - no Open
564 2.626611580182352 -0.738634 -20.7231 7 15 0 0.00 0.00 - no Open
560 2.7895108040750816 -0.957168 -24.9089 7 18 0 0.00 0.00 - no Open
548 4.529608506315844 -1.15162 -28.6945 10 21 0 0.00 0.00 - no Open
541 5.26808969809745 -0.966454 -25.0402 8 18 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 -30.513kcal/mol
Ligand efficiency (LE) -1.0522kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.044
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 447.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.33
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 19.51kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -14.53kcal/mol
Minimised FF energy -34.04kcal/mol

SASA & burial

✓ computed
SASA (unbound) 675.9Ų
Total solvent-accessible surface area of free ligand
BSA total 616.9Ų
Buried surface area upon binding
BSA apolar 489.4Ų
Hydrophobic contacts buried
BSA polar 127.5Ų
Polar contacts buried
Fraction buried 91.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.3%
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 1472.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)