FAIRMol

Z50138312

Pose ID 3804 Compound 2556 Pose 418

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
T06
T. brucei DHFR T. brucei
Ligand Z50138312
PDB8RHT↗

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 strong SASA done
Strain ΔE
19.8 kcal/mol
Protein clashes
3
Internal clashes
4
Native overlap
contact recall 0.62, Jaccard 0.50, H-bond role recall 0.00
Burial
92%
Hydrophobic fit
85%
Reason: no major geometry red flags detected
3 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.755 kcal/mol/HA) ✓ Good fit quality (FQ -7.49) ✓ Deep burial (92% SASA buried) ✓ Lipophilic contacts well-matched (85%) ✗ Moderate strain (19.8 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (3) ✗ Many internal clashes (17)
Score
-24.910
kcal/mol
LE
-0.755
kcal/mol/HA
Fit Quality
-7.49
FQ (Leeson)
HAC
33
heavy atoms
MW
438
Da
LogP
3.72
cLogP
Strain ΔE
19.8 kcal/mol
SASA buried
92%
Lipo contact
85% BSA apolar/total
SASA unbound
723 Ų
Apolar buried
563 Ų

Interaction summary

HB 1 HY 24 PI 4 CLASH 4

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

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

HY · Hydrophobic contacts

CLASH · Clashes
Final rank1.606Score-24.910
Inter norm-0.762Intra norm0.006
Top1000noExcludedno
Contacts18H-bonds1
Artifact reasongeometry warning; 17 clashes; 3 protein contact clashes; 1 cofactor-context clash
Residues
ALA34 ARG100 ARG59 ASP54 GLN56 GLU50 ILE47 LEU90 LEU97 MET55 NDP301 PHE58 PHE94 PRO52 PRO91 TYR57 VAL32 VAL33

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name8RHTContacts21
PoseOpen native poseHB0
IFP residues
ALA34 ASP54 HIS182 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE233 PHE58 PHE94 PRO91 SER89 THR184 THR86 TRP49 TYR166 TYR57 VAL32 VAL33
Current overlap13Native recall0.62
Jaccard0.50RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

223 residues
Protein targetT06Atoms3452
Residues223Chains1
Residue summaryARG:408; VAL:352; LYS:308; LEU:304; PRO:238; ILE:209; GLU:195; THR:182; SER:176; ALA:160; PHE:140; ASN:126; GLY:126; ASP:108; GLN:85; NDP:74

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
A:NDP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
418 1.606051960050609 -0.762141 -24.9103 1 18 13 0.62 0.00 - no Current
425 2.011850934217598 -0.799596 -25.6315 4 19 0 0.00 0.00 - no Open
445 2.940249651763982 -0.79876 -25.4429 1 18 1 0.05 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 -24.910kcal/mol
Ligand efficiency (LE) -0.7549kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.490
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 438.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.72
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 19.78kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -81.35kcal/mol
Minimised FF energy -101.13kcal/mol

SASA & burial

✓ computed
SASA (unbound) 723.1Ų
Total solvent-accessible surface area of free ligand
BSA total 661.4Ų
Buried surface area upon binding
BSA apolar 562.6Ų
Hydrophobic contacts buried
BSA polar 98.7Ų
Polar contacts buried
Fraction buried 91.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 85.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1834.0Ų
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 1808.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 598.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)