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 high
Native strong
SASA done
Strain ΔE
19.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.76, Jaccard 0.70, H-bond role recall 0.36
Reason: no major geometry red flags detected
1 protein-contact clashes
47% of hydrophobic surface appears solvent-exposed (8/17 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 (-1.279 kcal/mol/HA)
✓ Good fit quality (FQ -11.29)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (86% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Moderate strain (19.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-29.419
kcal/mol
LE
-1.279
kcal/mol/HA
Fit Quality
-11.29
FQ (Leeson)
HAC
23
heavy atoms
MW
315
Da
LogP
1.60
cLogP
Interaction summary
HB 12
HY 13
PI 1
CLASH 1
⚠ Exposure 47%
Interaction summary
HB 12
HY 13
PI 1
CLASH 1
⚠ Exposure 47%
Partial hydrophobic solvent exposure
47% of hydrophobic surface appears solvent-exposed (8/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 9
Exposed 8
LogP 1.6
H-bonds 12
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 4.106 | Score | -29.419 |
|---|---|---|---|
| Inter norm | -1.399 | Intra norm | 0.120 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 12 |
| Artifact reason | geometry warning; 10 clashes; 3 protein clashes | ||
| Residues |
ALA24
ALA40
ASN41
GLN42
GLU21
GLU73
GLY23
GLY25
GLY71
LEU39
LYS127
LYS159
LYS26
PHE38
SER22
SER27
SER28
THR44
| ||
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 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| 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 | 16 | Native recall | 0.76 |
| Jaccard | 0.70 | RMSD | - |
| HB strict | 5 | Strict recall | 0.33 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 5 | HB residue recall | 0.45 |
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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 623 | -0.21493581621955696 | -1.3166 | -29.3146 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 636 | 1.9065028710157321 | -0.990453 | -18.7513 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 638 | 2.078718061437694 | -1.03904 | -19.278 | 6 | 14 | 1 | 0.05 | 0.00 | - | no | Open |
| 640 | 2.4645938733667183 | -1.04408 | -17.2106 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 629 | 3.425746121157447 | -1.25604 | -25.7731 | 12 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 625 | 3.6012935560196184 | -1.2648 | -22.3059 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 648 | 4.1058842412556915 | -1.39928 | -29.419 | 12 | 18 | 16 | 0.76 | 0.36 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.419kcal/mol
Ligand efficiency (LE)
-1.2791kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.289
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
315.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.60
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.04kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
81.50kcal/mol
Minimised FF energy
62.46kcal/mol
SASA & burial
✓ computed
SASA (unbound)
547.0Ų
Total solvent-accessible surface area of free ligand
BSA total
470.8Ų
Buried surface area upon binding
BSA apolar
354.5Ų
Hydrophobic contacts buried
BSA polar
116.3Ų
Polar contacts buried
Fraction buried
86.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1282.7Ų
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
1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
515.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)