FAIRMol

Z31243438

Pose ID 492 Compound 47 Pose 492

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 Z31243438
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 high Native strong SASA done
Strain ΔE
11.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.62, Jaccard 0.54, H-bond role recall 0.00
Burial
94%
Hydrophobic fit
64%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.440 kcal/mol/HA) ✓ Good fit quality (FQ -12.05) ✓ Good H-bonds (3 bonds) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (64%) ✗ Moderate strain (11.0 kcal/mol) ✗ Geometry warnings
Score
-28.807
kcal/mol
LE
-1.440
kcal/mol/HA
Fit Quality
-12.05
FQ (Leeson)
HAC
20
heavy atoms
MW
304
Da
LogP
2.16
cLogP
Strain ΔE
11.0 kcal/mol
SASA buried
94%
Lipo contact
64% BSA apolar/total
SASA unbound
513 Ų
Apolar buried
308 Ų

Interaction summary

HB 3 HY 24 PI 2 CLASH 1
Final rank0.669Score-28.807
Inter norm-1.372Intra norm-0.068
Top1000noExcludedno
Contacts16H-bonds3
Artifact reasongeometry warning; 3 clashes; 1 protein clash
Residues
ALA10 GLU31 ILE8 LEU23 LEU28 LEU68 NAP201 PHE32 PHE35 THR137 THR57 TRP25 TYR122 TYR34 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 overlap13Native recall0.62
Jaccard0.54RMSD-
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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
483 -0.1611764887493698 -1.37577 -28.9243 3 16 13 0.62 0.00 - no Open
492 0.6689356312754727 -1.37192 -28.8074 3 16 13 0.62 0.00 - no Current
414 2.4961177081167616 -1.52147 -26.2739 13 17 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 -28.807kcal/mol
Ligand efficiency (LE) -1.4404kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.053
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 20HA

Physicochemical properties
Molecular weight 304.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.16
Lipinski: ≤ 5
Rotatable bonds 2

Conformational strain (MMFF94s)
Strain energy (ΔE) 10.99kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 13.08kcal/mol
Minimised FF energy 2.09kcal/mol

SASA & burial

✓ computed
SASA (unbound) 513.1Ų
Total solvent-accessible surface area of free ligand
BSA total 482.2Ų
Buried surface area upon binding
BSA apolar 307.7Ų
Hydrophobic contacts buried
BSA polar 174.5Ų
Polar contacts buried
Fraction buried 94.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 63.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1406.8Ų
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 608.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)