FAIRMol

Z20253414

Pose ID 545 Compound 2 Pose 545

DB SELECTIONDocking 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
T01
Human DHFR Human
Ligand Z20253414
PDB5SD8↗

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 strong SASA done
Strain ΔE
18.6 kcal/mol
Protein clashes
0
Internal clashes
4
Native overlap
contact recall 0.71, Jaccard 0.62, H-bond role recall 0.00
Burial
88%
Hydrophobic fit
76%
Reason: no major geometry red flags detected
4 intramolecular clashes 35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.062 kcal/mol/HA) ✓ Good fit quality (FQ -9.78) ✓ Good H-bonds (5 bonds) ✓ Deep burial (88% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Moderate strain (18.6 kcal/mol) ✗ Geometry warnings
Score
-27.601
kcal/mol
LE
-1.062
kcal/mol/HA
Fit Quality
-9.78
FQ (Leeson)
HAC
26
heavy atoms
MW
371
Da
LogP
2.19
cLogP
Strain ΔE
18.6 kcal/mol
SASA buried
88%
Lipo contact
76% BSA apolar/total
SASA unbound
652 Ų
Apolar buried
434 Ų

Interaction summary

HB 5 HY 21 PI 1 CLASH 0 ⚠ Exposure 35%
⚠️Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17 Buried (contacted) 11 Exposed 6 LogP 2.19 H-bonds 5
Exposed fragments: phenyl (2/5 atoms exposed)aliphatic chain/group (4 atoms exposed)
Final rank-0.197Score-27.601
Inter norm-1.009Intra norm-0.053
Top1000noExcludedno
Contacts18H-bonds5
Artifact reasongeometry warning; 4 clashes; 1 protein contact clash
Residues
ALA10 ASP22 GLU31 GLY21 ILE61 ILE8 LEU23 NAP201 PHE35 PRO26 PRO27 PRO62 SER60 THR57 TRP25 TYR122 VAL116 VAL9

Protein summary

200 residues
Protein targetT01Atoms3128
Residues200Chains2
Residue summaryLYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91

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:NAP201

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5SD8Contacts21
PoseOpen native poseHB0
IFP residues
ALA10 ASN65 ASP22 GLN36 GLU31 GLY117 GLY21 ILE61 ILE8 LEU23 LEU68 NAP201 PHE32 PHE35 PRO62 SER60 THR137 THR57 TYR122 VAL116 VAL9
Current overlap15Native recall0.71
Jaccard0.62RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
545 -0.19688936144560998 -1.00883 -27.6012 5 18 15 0.71 0.00 - no Current
489 2.929054263771643 -1.0687 -27.2601 5 14 0 0.00 0.00 - no Open
514 3.9749964876293937 -0.911876 -25.92 6 13 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 -27.601kcal/mol
Ligand efficiency (LE) -1.0616kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.781
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 371.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.19
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 18.65kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -74.23kcal/mol
Minimised FF energy -92.88kcal/mol

SASA & burial

✓ computed
SASA (unbound) 652.0Ų
Total solvent-accessible surface area of free ligand
BSA total 571.8Ų
Buried surface area upon binding
BSA apolar 433.8Ų
Hydrophobic contacts buried
BSA polar 137.9Ų
Polar contacts buried
Fraction buried 87.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1542.0Ų
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 1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 633.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)