FAIRMol

Z19041503

Pose ID 12664 Compound 2625 Pose 463

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 Z19041503
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
22.0 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.30, Jaccard 0.20, H-bond role recall 0.00
Burial
94%
Hydrophobic fit
80%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.842 kcal/mol/HA) ✓ Good fit quality (FQ -8.04) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ High strain energy (22.0 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (9) ✗ Many internal clashes (13)
Score
-24.414
kcal/mol
LE
-0.842
kcal/mol/HA
Fit Quality
-8.04
FQ (Leeson)
HAC
29
heavy atoms
MW
450
Da
LogP
4.15
cLogP
Strain ΔE
22.0 kcal/mol
SASA buried
94%
Lipo contact
80% BSA apolar/total
SASA unbound
635 Ų
Apolar buried
482 Ų

Interaction summary

HB 6 HY 16 PI 0 CLASH 5

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
Final rank1.857Score-24.414
Inter norm-1.112Intra norm0.265
Top1000noExcludedno
Contacts21H-bonds6
Artifact reasongeometry warning; 13 clashes; 9 protein contact clashes; moderate strain Δ 22.0
Residues
ARG287 ASP327 CYS52 CYS57 GLU202 GLY161 GLY56 ILE199 LEU334 LYS60 MET333 NDP800 PHE182 PHE203 PHE367 PRO336 SER14 SER162 SER178 THR335 THR51

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
Jaccard0.20RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
463 1.857417542478169 -1.11162 -24.414 6 21 8 0.30 0.00 - no Current
471 2.6502164879487613 -0.871671 -21.5801 2 19 0 0.00 0.00 - no Open
480 4.489730344288321 -1.07245 -29.0277 8 21 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 -24.414kcal/mol
Ligand efficiency (LE) -0.8419kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.036
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 450.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.15
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 89.84kcal/mol
Minimised FF energy 67.84kcal/mol

SASA & burial

✓ computed
SASA (unbound) 635.2Ų
Total solvent-accessible surface area of free ligand
BSA total 599.3Ų
Buried surface area upon binding
BSA apolar 481.8Ų
Hydrophobic contacts buried
BSA polar 117.5Ų
Polar contacts buried
Fraction buried 94.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3097.7Ų
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 1484.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)