Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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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
31.2 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.81, Jaccard 0.61, H-bond role recall 0.45
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
42% of hydrophobic surface appears solvent-exposed (8/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.082 kcal/mol/HA)
✓ Good fit quality (FQ -10.21)
✓ Good H-bonds (5 bonds)
✓ Deep burial (90% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Very high strain energy (31.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-30.290
kcal/mol
LE
-1.082
kcal/mol/HA
Fit Quality
-10.21
FQ (Leeson)
HAC
28
heavy atoms
MW
462
Da
LogP
3.91
cLogP
Final rank
4.7900
rank score
Inter norm
-1.245
normalised
Contacts
24
H-bonds 8
Interaction summary
HBD 1
HBA 4
HY 3
PI 1
CLASH 5
Interaction summary
HBD 1
HBA 4
HY 3
PI 1
CLASH 5
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| Name | RAB5A | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU21
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
| ||
| Current overlap | 17 | Native recall | 0.81 |
| Jaccard | 0.61 | RMSD | - |
| HB strict | 7 | Strict recall | 0.47 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 5 | HB residue recall | 0.45 |
Protein summary
165 residues
| Protein target | T22 | Atoms | 2561 |
|---|---|---|---|
| Residues | 165 | Chains | 1 |
| Residue summary | LEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 502 | 1.9757455555586445 | -1.15813 | -26.4706 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 538 | 2.343113533288865 | -0.858445 | -19.2476 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 510 | 2.360233268669932 | -1.11518 | -31.4922 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 526 | 4.789968659526765 | -1.24524 | -30.2901 | 8 | 24 | 17 | 0.81 | 0.45 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-30.290kcal/mol
Ligand efficiency (LE)
-1.0818kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.212
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
462.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.91
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
13.01kcal/mol
Minimised FF energy
-18.17kcal/mol
SASA & burial
✓ computed
SASA (unbound)
665.3Ų
Total solvent-accessible surface area of free ligand
BSA total
595.2Ų
Buried surface area upon binding
BSA apolar
468.1Ų
Hydrophobic contacts buried
BSA polar
127.1Ų
Polar contacts buried
Fraction buried
89.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1392.0Ų
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
1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
504.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)