FAIRMol

Z235511374

Pose ID 12689 Compound 13 Pose 488

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 Z235511374
PDB2WOV↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
40.6 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.30, Jaccard 0.21, H-bond role recall 0.20
Burial
94%
Hydrophobic fit
70%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.192 kcal/mol/HA) ✓ Good fit quality (FQ -10.35) ✓ Good H-bonds (5 bonds) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Extreme strain energy (40.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-26.221
kcal/mol
LE
-1.192
kcal/mol/HA
Fit Quality
-10.35
FQ (Leeson)
HAC
22
heavy atoms
MW
331
Da
LogP
3.44
cLogP
Final rank
1.4923
rank score
Inter norm
-1.471
normalised
Contacts
19
H-bonds 7
Strain ΔE
40.6 kcal/mol
SASA buried
94%
Lipo contact
70% BSA apolar/total
SASA unbound
535 Ų
Apolar buried
352 Ų

Interaction summary

HBD 1 HBA 4 PC 1 HY 6 PI 0 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

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
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: 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 overlap8Native recall0.30
Jaccard0.21RMSD-
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
498 0.277110928238548 -1.1663 -24.1398 5 15 0 0.00 0.00 - no Open
543 0.2814085707376848 -1.28181 -23.8629 6 18 0 0.00 0.00 - no Open
497 0.3261405134134158 -1.12693 -25.036 1 16 0 0.00 0.00 - no Open
523 0.7425493178553388 -1.13066 -24.5514 11 14 0 0.00 0.00 - no Open
523 1.118607833921333 -1.20811 -22.5833 5 14 0 0.00 0.00 - no Open
510 1.3649241206005485 -1.15 -20.093 5 15 0 0.00 0.00 - no Open
488 1.4922564307741122 -1.4707 -26.2212 7 19 8 0.30 0.20 - no Current
560 1.7657177566461795 -1.1595 -25.6991 7 16 0 0.00 0.00 - no Open
505 2.3175673752518597 -0.992997 -20.4526 5 11 0 0.00 0.00 - no Open
482 2.392174964889073 -1.5365 -31.914 7 15 0 0.00 0.00 - no Open
502 2.4832411156841925 -1.46125 -30.4633 8 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 -26.221kcal/mol
Ligand efficiency (LE) -1.1919kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.348
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 22HA

Physicochemical properties
Molecular weight 331.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.44
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 40.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 35.63kcal/mol
Minimised FF energy -4.97kcal/mol

SASA & burial

✓ computed
SASA (unbound) 535.5Ų
Total solvent-accessible surface area of free ligand
BSA total 503.4Ų
Buried surface area upon binding
BSA apolar 352.2Ų
Hydrophobic contacts buried
BSA polar 151.2Ų
Polar contacts buried
Fraction buried 94.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2970.7Ų
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 1469.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)